The seismic collapse-resistant capacity of the three-dimensional (3D) parking structure with alternation story-height truss lateral-load-resisting system was evaluated by IDA-based seismic fragility analysis method. The structural collapse process and mechanism under earthquake were analyzed. The seismic collapse-resistant capacities of the structure under one-directional and bi-directional earthquakes were compared. And the comparison of the seismic collapse-resistant capacities and collapse margin ratios of the structures with different floors was carried out. The result has shown that the seismic collapse-resistant performance of this kind of 3D parking structure is very good, and the first storey is the weak storey. The collapse probability increases with the increase of the storey count of the structure, and then the seismic performance becomes weak. However, the collapse margin ratio of the structure does not always decrease with the increase of the storey count of the structure. It is recommended that the provision of the height-width ratio in the current design code of building structure can be broken in the design of this kind of 3D parking structure.