Rail transit hubs naturally have advantages in terms of pedestrian flow. The development of multi-dimensional, mixed-use commercial spaces above these hubs has become a new construction model. The commercial spaces above rail transit hubs have become important places for passengers, commuters, and citizens to engage in consumption and social activities. The development of commercial spaces above most rail transit hubs is often large-scale, with complex spatial organization. This can lead to issues such as mismatched functional requirements, insufficient supply of service facilities, chaotic flow organization, low transfer efficiency, and poor spatial quality, resulting in insufficient guidance of pedestrian flow and low space utilization, which affects the vitality of commercial spaces and thus affects the healthy operation of commercial spaces. Therefore, this paper starts with the research on the vitality of commercial space above the rail transit hub. Firstly, it categorized the constituent elements of these commercial spaces, defining them in terms of functional organization, flow organization, and spatial construction across three dimensions. Then, two already constructed rail transit hub commercial spaces in China were selected for case study. Through field research and sample space screening, 15 indicators corresponding to the three dimensions were identified. The data analysis methods such as space syntax theory and SPSS correlation analysis were used to quantify the indicators. The study found that spatial vitality does not show a direct correlation with functional density, but it does exhibit a strong correlation with most flow organization indicators and all spatial construction indicators. The key factors influencing spatial vitality include functional density, spatial accessibility and visibility, entrances and exits, vertical transportation, and the location of resting areas. Finally, the specific operation of the design strategy was put forward in combination with the commercial space above the Chengdu station. The research content of this paper provides a design reference for the related design of the commercial space above the rail transit hub and offers new insights into related theoretical explorations.