Urban air mobility (UAM) extends urban transportation to low-altitude airspace using electric vertical take-off and landing (eVTOL) vehicle to reduce traffic congestion. The vertical take-off and landing (VTOL) site connecting ground and air transport is the critical infrastructure of the UAM. Determining its locations is essential for the design and operation of the air route. This study focuses on the problem of the location of the VTOL site, using Shenzhen as the study area, and establishes an integer programming model with the objective of maximizing travel cost savings to identify the optimal locations of the VTOL sites. This study is different from existing ones in that it explicitly considers the three-dimensional spatial availability of VTOL sites. Geographic information system (GIS) tools are used to identify locations that satisfy two-dimensional (2D) planar availability, and an obstacle assessment model of the approach/departure and transitional surfaces of the VTOL site is built to further screen the locations. The selected potential sites are used as input to the integer programming model, ensuring that the locations identified to establish the VTOL site are optimal. The impact of the number of VTOL sites, the user's transfer time at the VTOL sites, and the eVTOL pricing on the model solution is also discussed. Although this study uses Shenzhen as a research object, the proposed methodology is generalized and applicable to any other city or region, providing recommendations and references for initial planning and related operations of the UAM in selected areas.