This paper proposes a novel spatial equilibrium model integrating station locations of intercity high-speed rail (HSR), which allows for households.intracity commuting, intercity migration, and intercity commuting. The proposed model explicitly investigates the effects of station location on urban spatial structure, households. choices of residence and workplace, and housing market. We systematically analyze and summarize all spatial structures for two cities, as a result of a great diversity of station location. The analysis result reveals that station location will affect households.choices of residence and workplace, and administration will underestimate travel demand when ignoring intercity commuting due to population migration. Numerical results indicate that although the reconstruction of existing stations is not the best scheme for household utility, it may be the best one for social welfare from the perspective of saving demolition costs. It is also found that the improvement of intercity transport between specific cities may lead to population migration to lower-income cities and then flatten the urban population and housing rental prices of higher-income cities.