Abstract: Agricultural green total factor productivity (AGTFP) has been widely used to optimize cropland spatial layout in sustainable agriculture. This study aims to systematically investigate the spatiotemporal evolution of cropland landscape fragmentation and AGTFP in China from 2000 to 2022. Land use data was collected from 285 Chinese cities. ArcGIS 10.8 and Fragstats 4.2 platforms were employed to measure cropland landscape fragmentation from three dimensions: scale, regularity, and agglomeration. Spatiotemporal evolution of fragmentation was subsequently analyzed after measurement. A super-efficient unconditional SBM-GML model was used to estimate AGTFP and the contribution rates of technical efficiency. Spatiotemporal patterns of AGTFP were then examined. Furthermore, a double fixed effect model and a spatial econometric model were employed to clarify the spatial impact of cultivated land landscape fragmentation on AGTFP and its spatial spillover effects. A systematic investigation was implemented to explore the heterogeneous effects of cropland landscape fragmentation on AGTFP, particularly from the perspective of scale, regularity, and agglomeration. The results indicated that: (1) Cropland landscape fragmentation index increased from 0.4802 to 0.5008 from 2000 to 2022, indicating the spatial shift of distribution pattern from east to west. The Loess Plateau and Yunnan-Guizhou Plateau emerged as severe fragmentation hotspots, while the central regions experienced increasingly outstanding fragmentation. The increasing rate of cropland landscape fragmentation decelerated slightly after 2020, indicating a notable weakening trend. (2) The AGTFP showed a steady upward trend, with technological progress as the main driving force. Spatially, there was a changing trend of “leading in the east, rapid development in the middle, and steady improvement in the west”. The AGTFP in the central region increased rapidly after 2010, and the high-level areas gradually spread to the west. (3) There was a negative impact of cropland landscape fragmentation on AGTFP, with an outstanding spatial spillover effect. Among them, the spatial spillover effect in the eastern region was significantly stronger than that in the central and western regions. The main grain-producing areas eliminated the negative impact internally, while the production and marketing balance areas were difficult to achieve regional compensation, due to double constraints. Regional heterogeneity stemmed from the various levels of economy, technological diffusion capacity, and geo-ecological conditions in eastern, central, and western China. The heterogeneity among grain functional zones was attributed to the differences in agricultural technology levels, the market strength, and the factor allocation capacity. The findings can provide a scientific basis to optimize the spatial layout of cultivated land in high-quality agriculture.