Abstract: Cropland scale, cropland fragmentation and other cropland resource endowment characteristics directly affect farmers’ cropland input behavior. It is significant to explore the influence mechanism of those resource endowment characteristics on farmers’ cropland ecological protection behaviors, in order to promote the cropland ecological protection and agricultural green transformation and upgrading. The research methods were to collect 434 valid data through a questionnaire survey of farmers in Changde City, a large agricultural city. On this basis, the effects of cropland scale and fragmentation of cropland on farmers’ cropland ecological protection behaviors were empirically tested by using the Tobit model with fertilizer and pesticide application as an example. At the same time, this paper refined the cropland scale into cropland management scale and plot scale, and explored the interaction between cropland management scale, plot scale, and cropland fragmentation. The results show that: 1) The deepening of the degree of cropland fragmentation will exacerbate the amount of fertilizer and pesticide applied by farmers, and promote the positive effect of cropland management scale on the amount of fertilizer and pesticide applied. This is not beneficial to the adoption of cropland ecological conservation behaviors by farmers. 2) The relationship between cropland management scale and the amount of fertilizer and pesticide applied is an inverted ‘U’-shaped. With the expansion of the cropland management scale, the fertilizer and pesticide application per unit sowing area of farmers shows an increasing trend, when the cropland management scale increases to a certain extent, the expansion of the cropland management scale will reduce the fertilizer and pesticide application. It is conducive to the adoption of cropland ecological protection measures by farmers. 3) The expansion of plot scale exerts a significant inhibitory effect on farmers’ fertilizer and pesticide application. 4) The expansion of plot scale can effectively mitigate the promoting effect of intensified cropland fragmentation on fertilizer and pesticide application, while also weakening the positive impact of cropland management scale expansion prior to the turning point. In conclusion, this study highlights the complex interplay between cropland fragmentation, management scale, and plot scale in shaping farmers’ input decisions. To advance cropland ecological protection, policies should encourage land consolidation to reduce fragmentation, promote appropriately scaled operations, and expand plot size through land merging and high-standard farmland construction. Simultaneously, differentiated technical training and incentives should be provided to key farmer groups to facilitate the adoption of green production practices.