As a frequently occurring natural disaster, drought will cause great damage to agricultural production and the sustainable development of a social economy, and it is vital to reasonably evaluate the comprehensive risk level of drought for constructing regional drought-resistant strategies. Therefore, to objectively expound the uncertainty of a drought risk system, the precondition cloud and maximum entropy principle coupling model (PCMEP) for drought risk assessment is proposed, which utilizes the principle of maximum entropy to estimate the probability distribution of cloud drops, and the two-dimensional precondition cloud algorithm to determine the certainty degree of drought risk. Moreover, the established PCMEP model is further applied in a drought risk assessment study in Kunming city covering 1956–2011, and the results indicate that (1) the probability of drought events for different levels exhibits a slight increasing trend among the 56 historical years; and (2) both the integrated certainty degree and its component of drought risk are more evident, which will be more beneficial to determine the drought risk level. In general, the proposed PCMEP model provides a new reliable idea to evaluate the comprehensive risk level of drought from a more objective and systematic perspective.