Abstract: Nano-colloidal particles are the basic units of soil aggregates and play an important supporting role in aggregate stability and water and fertilizer utilization. This study aims to systematically evaluate the regulatory effects of nano-clinoptilolite based nitrogen fertilizer on paddy soil aggregate structure, rice physiological characteristics, nitrogen utilization and yield formation. A field split-plot experiment was conducted, with two irrigation modes, conventional flooding (ICF) and alternate wetting and drying irrigation (IAWD) as the main factors, and three sub-factors including no nano-clinoptilolite based nitrogen fertilizer (Z₀N₁₀), 20% nano-clinoptilolite based nitrogen fertilizer & 80% urea (Z₂N₈), 40% nano-clinoptilolite based nitrogen fertilizer & 60% urea and (Z₄N₆). The nano-clinoptilolite based nitrogen fertilizer used in this study was prepared as follows: Clinoptilolite was dispersed in distilled water and subjected to ultrasonic pulverization. Following pulverization, the supernatant was collected and dried for at least 48 hours to obtain nano-sized clinoptilolite. The prepared nano clinoptilolite was then mixed with an ammonium chloride solution and allowed to adsorb for 2 hours, after which the supernatant was separated. Finally, the nano-clinoptilolite based nitrogen fertilizer was dried for more than 48 hours until completely dry. To investigate the effects of alternating wetting and drying irrigation and nano-clinoptilolite based nitrogen fertilizer on the composition of paddy soil aggregates, complete soil samples were collected from the 0～20 cm soil layer of each experimental plot using a five-point sampling method after rice harvest in 2022. After the soil samples were naturally air-dried, they were manually crushed into small pieces according to their natural structure and initially screened through a 10 mm sieve. Subsequently, each sample was graded through sieves of different apertures (5, 3, 2, 1, 0.5, and 0.25 mm). The results showed that the wet-dry changes of IAWD caused 1～<3 mm aggregates to break into micro-aggregates (increased by 16.79%) and reduced soil aggregate stability (4.67%). Nano clinoptilolite based nitrogen fertilizer effectively increased the proportion of >0.25 mm macroaggregates (6.26%～11.13%), enhanced soil structural stability (6.95%～17.72%) and inorganic nitrogen concentration (6.81%～14.77%). The application of nano-clinoptilolite based nitrogen fertilizer significantly increased the effective tillering rate (20.01%～29.99%), chlorophyll (11.06～28.97%) and yield (8.26%～16.65%) of rice. Nano-clinoptilolite based nitrogen fertilizer also increased the nitrogen accumulation threshold of plants (5.59%～12.47%) by increasing the inflection point accumulated temperature. Structural equation modelling revealed that the synergistic effect of 80% nano-clinoptilolite based nitrogen fertilizer mixed with 20% urea (Z₂N₈) was achieved through the path of soil aggregate structure optimization-nitrogen effective supply and absorption-nitrogen accumulation-driven yield improvement. This study provides technical support for green and efficient water-fertilization in northern rice fields.