The concept of a high-speed passenger traffic location line is proposed by analyzing intercity rail traffic location and network evolution characteristics to improve the effectiveness of intercity rail transit network layout planning. Then, a multilevel intercity rail transit network planning and optimization model is constructed. The model is divided into two levels, namely, the backbone network and the preliminary network. The backbone network optimization model is the minimum spanning tree model, which uses the reciprocal of economical relation intensity as its weight. The preliminary network model is a multi-objective function, which maximizes economical relation intensity and connectivity and minimizes the total length of rail transit lines. The optimization model provides a new method for intercity rail transit network planning. Finally, the rationality and effectiveness of the network layout are verified using the line network within the Wuhan urban agglomeration area as an example.