To solve the reasonable investment problems of handling equipment in container terminal, a mixed integer programming model is built with comprehensive consideration on investment cost and average handling efficiency. And a solution algorithm is established with genetic algorithm and system simulation. An experiment about handling equipment investment plan optimization in a container terminal is given to verify the validity of the model and feasibility of solution method. The results show that the model can optimize the handling equipment investment plan with comprehensive consideration on cost and efficiency. The solution algorithm can effectively improve the global search efficiency and the real investment effect.