Ecological compensation is an important means for controlling agricultural nonpoint source pollution, and compensation methods comprise an essential part of the compensation policy for mitigating this form of pollution. Farmers’ choice of compensation methods affects their response to compensation policies as well as the effects of pollution control and ecological compensation efficiency. This study divides ecological compensation methods into two distinct philosophies—the “get a fish” method (GFM) and “get a fishing skill” method (GFSM)—based on policy objectives, to determine farmers’ choice between the two methods and the factors influencing this choice. Furthermore, by analyzing survey data of 632 farmers in the Ankang and Hanzhong cities in China and using the multivariate probit model, the study determines farmers’ preferred option among four specific compensation modes of GFM and GFSM. The three main results are as follows. (1) The probability of farmers choosing GFM is 82%, while that of choosing GFSM is 51%. Therefore, GFM should receive more attention in compensation policies relating to agricultural nonpoint source pollution control. (2) Of the four compensation modes, the study finds a substitution effect between farmers’ choice of capital and technology compensations, capital and project compensations, material and project compensations, while there is a complementary relationship between the choice of material and technology compensations. Therefore, when constructing the compensation policy basket, attention should be given to achieving an organic combination of different compensation methods. (3) Highly educated, young, and male farmers with lower part-time employment, large cultivated land, and a high level of eco-friendly technology adoption and policy understanding are more likely to choose GFSM. Hence, the government should prioritize promoting GFSM for farmers with these characteristics, thereby creating a demonstration effect to encourage transition from GFM to GFSM.