Based on process feature of the practical diffuser shops, the model of the fuzzy flexible job-shop scheduling problem of various batches was given, considering the various resource constraints including moulds, machines and operators and the uncertainty factors of processing time and due date. Integrating multi-agent system and the immunity information processing mechanism of immune system in biotic science, an approach of multi-agent immune algorithm was proposed to solve the pratical job-shop scheduling problem. It mainly consisted of several operators: competition operator among the agent and its neighbors, self-study operator of the optimal agent, adaptive bacterin extraction and vaccination operator, cross and mutation operator, and simulated annealing operator. The position of the agent was updated with those operators in the solution space, and thus it would accurately search the global optimal. Then, the multi-agent immune algorithm was applied to solve a scheduling example from a certain diffuser shop, and the results showed its validity.