The original equipment manufacturing mode of the multi-species, multi-process and multi-unit is the main mode in Zhejiang manufacturing industry, the workshop layout affect directly the production efficiency and cost. The paper analyzed the impact factors of discrete operations workshop layout, established the Multi-Agent mathematical model of discrete operations workshop layout by using Multi-Agent theory, put forward the objective function of the workshop layout, and carried out empirical study by typical enterprises. By analyzing raw data of ZJ manufacturing enterprise, brought forward two layout programs based on mathematical model of Multi-Agent, evaluated the benefits and chose the better one of the two programs according to the objective function. The results after the implementation showed that the logistics measuring pitch of the program after selection is small, and the workshop area utilization is higher, and the equipment cost is reasonable. The model and optimization technology of discrete operations workshop layout based on Multi-Agent theory has important practical significance and good feasibility.