This paper takes 994 overseas enterprises established by around 838 domestic companies as China’s overseas agricultural investment by 2014 as samples, using location advantages reflecting the host country and institutional factors as the main survey variables, considers comprehensively other factors such as the geographic distance and agricultural trade between host country and China, telecommunication capacity, selects 12 independent variables, and applies Conditional Logit model to study their impact on the location decision making of China’s overseas agricultural investment, and also explore influencing factors of agricultural investment in the links of production and operation. Analysis indicates that such factors including endorsement of agricultural natural resources and market potential in the host country have significant impact on agricultural FDI attraction. The quality of host countries’ economic and legal institutions has significant effect on agricultural FDI location choice; but the quality of political institutions has a negative effect. The openness of agricultural FDI, trade dependence of agricultural products, telecommunication capacity in the host country as well as geographic distance with China are also obviously correlated with location choices of China’s overseas agricultural investment. The results also suggest there are more common factors than decisive factors on location choice of China’s overseas agricultural investment in the links of production and operation.