In the process of clinker calcination, the target value of the raw meal decomposition rate (RMDR) is different in the easy and difficult calcination stages because the boundary conditions of raw meal (i.e., raw meal flow, raw meal ingredients, and particle size) change frequently, where RMDR cannot be guaranteed to be within its desirable range. To solve this problem, an intelligent setting control method is proposed in this paper for a clinker calcination process. The proposed approach is realized by on-line adjustment of the setpoints of control loops in line with the changes of raw meal boundary conditions. This method consists of five modules, namely an RMDR target value setting model, a control loop pre-setting model, a feedback compensation model based on the fuzzy rules, a feedforward compensation model based on the fuzzy rules, and a soft measurement model for RMDR. Successful application to the clinker calcination process of the Jiuganghongda Cement Plant in China has been made, where the efficiency of the proposed method has been validated by the results of the practical application.