Research conclusions：Set pair analysis theory is a new method to deal with the uncertain and multiplex problems. Through quantitatively analyzing uncertain systems and sequencing the uncertainness of the different programs, the optimum program is obtained by establishing the integrated evaluation model for rail transit in Lagos with the set pair analysis theory, determining the index weight with analytic hierarchy process and establishing the evaluation index system for evaluation and estimation of a number of optional programs. The results show that the set pair analysis theory can be used for optimizing the track program of rail transit.