Abstract: In the light of continued urbanization, it is important to analyze the effect of urbanization on fertilizer non-point source pollution in China to alleviate ecological pressure and promote green and high-quality agriculture development. This study used the unit survey and assessment method to measure the total emissions and emission intensity of fertilizer non-point source pollution in 31 provinces (cities, autonomous regions) in China from 2008 to 2018. The mediation effect model was used to analyze the influence of urbanization on fertilizer non-point source pollution. Compared with existing studies, this study has two aims. The first is to analyze the influence of urbanization on fertilizer non-point source pollution via the mediation effect, and to clarify the mechanism of how urbanization affects fertilizer non-point source pollution. The second is to analyze the spatial heterogeneity in the impact of urbanization on the fertilizer non-point source pollution in grain function areas, e.g., differences in the mechanisms of various mediation factors in different grain function areas. Our empirical results showed that: 1) from 2008 to 2018, fertilizer non-point source pollution in China had an inverted “U” pattern, first increasing and then decreasing, with 2015 as the inflection point. The total amount and intensity of emissions fell to the lowest levels at the end of the study period, 5.16 million t and 37.65 kg·hm⁻², respectively. 2) On a national level, urbanization had a mediating effect on fertilizer non-point source pollution owing to technological progress, labor migration, and farmland endowment. The mediation effect of farmland endowment had the highest absolute value (0.0092), and the mediation effects of labor and technological progress were increasing to 0.0040 and 0.0033, respectively. 3) There was significant spatial heterogeneity in the influence of urbanization on fertilizer non-point source pollution. For technological progress, the absolute value of the mediation effect in the major grain-consuming areas was the highest (0.0160), followed by that in the major grain-producing areas (0.0118), whereas the grain-balance areas did not have a significant mediation effect. For labor, there was only a significant mediation effect in the major grain-production areas (0.0538). For farmland endowment, the absolute value of the mediation effect in the major grain-consuming areas was the highest (0.0126), followed by that in the grain-balance areas (0.0095), and the major grain-producing areas had the lowest absolute value (0.0055). The direction of the mediation effect in grain-balance areas was opposite to that in other regions. Therefore, it was important to protect arable land in the major grain-consuming areas and to form a cross-regional collaboration system of “occupation-compensation balance”. In the major grain-producing areas, high-quality labor should be actively guided to return to the agricultural sector. In the grain-balance areas, green agricultural technology and management modes should be introduced.