Abstract: The problem of non-point source (NPS) fertilizer pollution caused by unscientific and irrational fertilizer inputs is becoming increasingly serious. The cultivated land is the most basic and scarce resource for agricultural production, its’ scale and fragmentation directly restricts the fertilizer input behavior of farmers. Therefore, it is important to investigate the influence of cultivated land scale, fragmentation, and other resource endowment characteristics of cultivated land on fertilizer NPS pollution, which is important for controlling chemical fertilizer NPS pollution and promoting the green transformation and sustainable development of agriculture. Unlike other studies that only focus on the impact of cultivated land operation scale or cultivated land fragmentation on fertilizer input or fertilizer use efficiency, this study, from the perspective of micro-farmers, subdivided cultivated land scale into operation scale and plot scale, and rationalized the relationship between cultivated land operation scale and fragmentation, and plot scale, and their impact mechanisms on fertilizer NPS pollution at a theoretical level. Based on the questionnaire survey data of farmers in the Dongting Lake area, the fertilizer NPS pollution intensity generated by fertilizer inputs in the agricultural production process of farmers was measured using inventory analysis. Tobit model was used to empirically analyze the impacts of cultivated land scale and fragmentation on fertilizer NPS pollution. The results showed that: 1) there was a significant positive correlation between cultivated land fragmentation and fertilizer NPS pollution. The higher the degree of cultivated land fragmentation, the higher the fertilizer NPS pollution intensity, and the deepening of cultivated land fragmentation could weaken the effect of cultivated land operation scale expansion and plot scale expansion on fertilizer NPS pollution reduction. 2) The relationship between the scale of cultivated land operation and fertilizer NPS pollution intensity was “U” shaped. The fertilizer NPS pollution intensity tended to decrease and then increase with the expansion of the cultivated land operation scale, with an inflection point of 4.311 hm². The expansion of the cultivated land operation scale also weakened the negative effect of cultivated land fragmentation and strengthened the positive effect of plot size expansion on reducing fertilizer NPS pollution. 3) Plot size significantly affected fertilizer NPS pollution. The expansion of the plot scale was conducive to the reduction of fertilizer NPS pollution. At the same time, the expansion of the plot scale could effectively regulate the negative effect of cultivated land fragmentation on the reduction of fertilizer NPS pollution and enhance the positive effect of the expansion of cultivated land operation scale on the reduction of fertilizer NPS pollution. Consequently, to reduce NPS fertilizer pollution, the government should combine land consolidation with land transfer and encourage farmers to expand the scale of cultivated land operations within an appropriate scope. At the same time, it is necessary to promote the expansion of the plot scale and reduce the degree of land fragmentation, leading to the effective use of cultivated land.