Flexible job-sop scheduling problem (FJSP) is based on the classical job-shop scheduling problem (JSP). however, it is even harder than JSP because of the addition of machine selection process in FJSP. An improved artificial immune algorithm, which combines the stretching technique and clonal selection algorithm is proposed to solve the FJSP. The algorithm can keep workload balance among the machines, improve the quality of the initial population and accelerate the speed of the algorithm’s convergence. The details of implementation for the multi-objective FJSP and the corresponding computational experiments are reported. The results indicate that the proposed algorithm is an efficient approach for the multi-objective FJSP.