Abstract: Current literature offers no thorough investigation into eVTOL vertiport allocation and pricing. A critical gap exists for a mechanism to boost social welfare while ensuring truthful bidding and market monopoly prevention. This paper constructs an eVTOL vertiport allocation model based on VCG auction theory, with Shenzhen as a case study. Through experimental simulations, we compared the performance of one-shot combinatorial (O-VCG) auction and sequential VCG auction (S-VCG) across various market environments, with focus on how vertiport quantity, operator bidding behavior, cross-regional package preferences, and regional partition granularity affect resource allocation efficiency. The experimental results demonstrate that the optimal auction mechanism depends on the market environment and agent characteristics: (1) Auction mechanisms, especially S-VCG auction, outperform fixed pricing mechanisms in terms of social welfare. While the latter can boost short-term platform revenue, they suppress agents’ profits and market participation. (2) Partitioned auctions show greater robustness in most scenarios: S-VCG comprehensively outperforms O-VCG in platform revenue and achieves higher social welfare when resources are abundant or bidding activity is high. (3) An optimal granularity exists for regional division: Increased regional quantity first promotes but later suppresses social welfare, which indicates the need to balance competition incentives with match efficiency. This study provides low-altitude economy regulators with a scientific resource allocation tool and decision basis founded on auction theory, and confirms the substantial potential of mechanism design to address complex airspace resource management problems.