This research is seeking to explore one set of system and method, which is more scientific, feasible and professional, dedicated to be applied to the performance evaluation of logistics enterprises.It introduced the balanced score card idea to establish a performance evaluation system and thus avoids the traditional limitation of only focused on financial indexes.It further advocated using the analytic hierarchy process and the principal component analysis to construct an novel evaluation model.It consequently achieves the goals of retaining the original information to the greatest extent based on demolishing the overlapped factors.Meanwhile, it incorporated the decision-makers subjective judgments on the authority of these indexes into the evaluation system.By this way, compared with the Model purely using the principal component analysis, it is capable of including both the objective information and humans subjective judgments, as a result, the evaluation conclusion is more dedicated and practical especially for those logistics enterprises whose operational and managing targets differ from each other.In the end, it identified the effectiveness and practicality of this model through an evaluation analysis.