This paper presents a mathematical methodology for transit route network optimization. The goal is to provide an effective computational tool for optimization of a large-scale transit route network. The objectives are to minimize transfers and maximize service coverage. Formulation of the method consists of three parts: representation of transit route network solution search spaces, representation of transit route and network constraints, and a stochastic search scheme capable of finding the expected global optimal result on the basis of an integrated simulated annealing, tabu, and greedy search algorithm. The methodology has been tested with published solutions to benchmark problems and applied to a large-scale realistic network optimization problem in Miami-Dade County, Florida.