Climate change not only affects agricultural output but also affects factor input of agricultural production. This paper empirically analyzes the impact of the change of temperature and rainfall on the demand of fertilizer in the production of crop farming by using the panel data of 26 provinces in China during 2001-2012, and the results show that on the whole yearly average temperature ascending is helpful to decrease the demand of fertilizer, but the increase of yearly average rainfall raises the demand of the fertilizer. In tropical and semitropical monsoon climate regions, both the increase of rainfall and the ascending of temperature can raise the demand of the fertilizer, however, in temperate monsoon zone, the ascending of temperature can decrease the demand of fertilizer, but the influence of rainfall increase on the demand of fertilizer is not significant. Climate change has different impacts on fertilizer input in agricultural production in different climate zones. Thus, the policy on controlling fertilizer is necessary to consider the impact of climate factor and its policy target should embody regional difference.