This work aimed to study the production scheduling optimization problem of enterprises orienting multi-varieties and small-batch orders. In view of the production status of company S, a scheduling optimization scheme was designed with genetic algorithm, using unequal length encoding matrix to accomplish the scheme of mass production and the scheduling of the workshop order. Through simulation analysis and actual trial of company S, the feasibility and effectiveness of the proposed algorithm were verified. The scheduling algorithm, which indeed realized the scheduling optimization of enterprises based on genetic algorithm, achieved the aim of shortening the production cycle and effectively utilizing production resource.