Abstract: Ecosystem fragmentation and biodiversity are declining in the sections of the Yellow River Basin in Shandong Province. It is often required for the zoning-based ecological conservation with categorical controls, in order to enhance the regional ecosystem services. In this study, the InVEST model was first employed to evaluate four key ecosystem services (ES): water yield, carbon storage, soil conservation, and habitat quality, over 77 counties in nine cities adjacent to the Yellow River in Shandong Province from 2002 to 2022. Subsequently, a self-organizing feature mapping (SOFM) model with a conventional K-means cluster was utilized for the cluster analysis. The ecosystem service bundles were then identified to validate the clustering of ecosystem service bundles. Finally, an econometric model of the panel data was applied to interpret the driving factors of the ecosystem service bundles (ESB). And the driving factors of four ecosystem services were adopted as fixed effects models (FEM) in econometrics, while random effects models (REM) were employed for the ESB-driven analysis. Furthermore, targeted ecological zoning control strategies for the Yellow River Basin in Shandong Province are proposed.The results revealed: 1) Spatiotemporal distribution. Water yield exhibited a stepped spatial gradient with the decrease from the central mountainous area to the main channel, and further to the western Shandong plain. Precipitation in the central mountainous region was significantly higher than in the rest areas. Carbon storage shared the higher values in the mountainous areas, whereas the lower values were found in the plains. Soil conservation displayed a hierarchical decline from the central mountainous area to the western plain and the Yellow River Delta. Habitat quality was highest in the central mountainous area, the Yellow River Delta, Dongping Lake, and Nansi Lake. While the urban agglomerations exhibited the lowest habitat quality. In terms of time span, the water yield capacity increased by 0.3% in 2022, compared with the 2002–2022 average. The carbon storage capacity decreased by 4.5% annually, compared with 2022; The soil conservation capacity was twice in 2022 as much was in 2002. The habitat quality remained largely unchanged with a 0.2% increase since 2002. 2) Ecosystem service bundles identification. According to the spatial distribution patterns of ecosystem services, the SOFM classified the 77 counties into four ESBs: ecological coordination, water conservation, ecological development, and urban development bundle. The urban development bundles evolved into the ecological ones, while purely urban development bundles decreased markedly in 2002-2007. Only a little significant change occurred in 2007-2012. Furthermore, the ecological development bundles decreased significantly, while the urban development bundles increased substantially in 2012-2017. Ecological development bundles increased markedly, whereas the urban development bundles decreased noticeably in 2017-2022. 3) Driving factors. Driving mechanisms indicated that the temperature, precipitation, population, and land development intensity exerted varying degrees on the ecosystem service bundles. Among them, there were significant negative effects of the temperature and land development intensity on the ESB changes. While the precipitation and population shared the positive effects. There was a significant variation in the dominant influencing factors on the different ecosystem service bundles. Therefore, the ecological measures should be implemented to tailor to the local conditions of each ecological functional zoning. 4) Zoning strategies. 77 counties were divided into six major zones: water conservation, core protection, dominant service, ecological enhancement, key protection, and ecological agriculture zone. Different strategies were proposed from the perspectives of ecological conservation and high-quality development. The zoning framework can provide the scientific support to mitigate the fragmentation for the spatial patterns optimization and ecological restoration in Shandong Province. Great contributions can also be achieved for the coordinated development of the ecological protection and socio-economic goals for the Yellow River Basin. Four types of ecosystem service bundles and the six major zoning schemes can be directly applied to the rest provinces within the Yellow River Basin, as well as to the major river systems across China. The spatially differentiated applicability and dissemination can also provide precise guidance for the decision-making on the regional production.