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The transit network design and frequency setting problem is related to the generation of transit routes with corresponding frequency schedule. Considering not only the influence of transfers but also the delay caused by congestion on passengers' travel time, a multi-objective transit network design model is developed. The model aims to minimize the travel time of passengers and minimize the number of vehicles used in the network. To solve the model belongs to a NP-Hard problem and is intractable due to the high complexity and strict constraints. In order to obtain the better network schemes, a multi-population genetic algorithm is proposed based on NSGA-II framework. With the algorithm, network generation, mode choice, demand assignment, and frequency setting are all integrated to be solved. The effectiveness of the algorithm which includes the high global convergence and the applicability for the problem is verified by comparison with previous works and calculation of a real-size case. The model and algorithm can be used to provide candidates for the sustainable policy formulation of urban transit network scheme. [ABSTRACT FROM AUTHOR]