Whether the business process and operational activities of the third party logistics (3PL) enterprise is coordinated and optimized is a key factor determining the operational efficiency of 3PL. Based on the value chain theory, a model of the business process optimization of 3PL cooperation is built. By analyzing the relationship between the business process and operational activities, how to allocate cost and value to operational activities is determined. In this way, the business activities with competitive advantages in the corporation are found, and the business process is further optimized accordingly, which can improve the operational efficiency of 3PL enterprise as a result. At last, a case study of business process optimization modeling for a 3PL enterprise that operates steel products is given to validate the effectiveness and practicability of this method.