The evaluation of service level for public transport is of great significance in urban traffic system management and operation construction. This paper establishes the indices system of service level through three aspects of sites, routes and public transport system on the basis of analyzing the existing evaluation research and considering the uncertainty and complexity in the process of systematic evaluation, and then on the basis of Set Pair Analysis (SPA), it establishes Set Pair Analysis Model ( SPAM) in public transportation system and introduces the identity- discrepancy- contrary ( IDC) connection degree formula which can embody certainties and uncertainties of the assessment system. It uses the AHP method to determine the weights of the indices. According to the calculation results of connection degree between indicators which the level of the evaluation system is determined . Finally, a simple example is given to illustrate the application of the method.