Rural residents’ willingness to shop online for agricultural inputs is an important basis for our country to guide the rational and orderly development of e-commerce market for rural agricultural input, which plays a significant role in the construction of agricultural modernization. Based on the theory of technology acceptance model and a survey data of rural residents in 17 provinces, this paper adopted the structural equation model and the hierarchical regression method to analyze rural residents’ willingness to shop online for agricultural inputs and the driving factors. Results show that 47.9% of rural residents do not know much about the forms of agricultural inputs online shopping, and only 18.7% of rural residents have strong willingness of online shopping. Perceived risks have significant inhibitory impacts on rural residents’ willingness to shop online for agricultural inputs. This is because rural residents have little experience of online shopping, leading to their resistance of online shopping. In addition, website service quality and subjective norms play significant roles in promoting rural residents’ willingness to shop online. Initial trust plays a mediating role in the relationship among perceived risks, website service quality, subjective norms, and rural residents’ online shopping intention of agricultural inputs. Initial trust could enhance the willingness of rural residents to shop online for agricultural inputs. In addition, farm scale and farming experience play a moderating role in the above relationship. In conclusion, this paper provides the following suggestions for those e-commerce enterprises: expanding the rural e-commerce market at different levels, reducing the perceived risks for rural residents’ online shopping for agricultural inputs, improving the quality of website services, establishing a good reputation, and enhancing rural residents’ willingness to shop online for agricultural inputs.