Abstract: Against the backdrop of global technological and industrial transformation, the low-altitude economy has emerged as a strategic frontier for reshaping regional competitiveness. However, existing studies offer no thorough investigation into the operational management issues associated with the allocation and pricing of electric vertical take-off and landing (eVTOL) vertiports. To address this gap, this paper designs an allocation and pricing mechanism that enhances social welfare, incentivizes truthful bidding, and mitigates market monopolization. An eVTOL vertiport allocation model based on Vickrey-Clarke-Groves (VCG) auction theory is developed, with Shenzhen as a case study. Through experimental simulations, the performance of the one-shot VCG auction (O-VCG) and the partitioned sequential VCG auction (S-VCG) is compared across various market environments, with focus on the impact of vertiport quantity, operator bidding behavior, cross-regional package preferences, and regional partition granularity on allocation efficiency. Experimental results demonstrate that the optimal auction mechanism depends on the market environment and agent characteristics. (1) Auction mechanisms, especially the S-VCG auction, outperform fixed pricing mechanisms in terms of social welfare. Although fixed pricing may increase short-term platform revenue, it reduces operator profits and market participation. (2) Partitioned auctions show greater robustness across most scenarios where S-VCG comprehensively outperforms O-VCG in platform revenue and achieves higher social welfare when resources are sufficient or bidding activity is high. (3) An optimal granularity exists for regional partition. Increasing regional quantity initially promotes but eventually suppresses social welfare, indicating the need to balance competition incentives with matching efficiency. This study provides low-altitude economy regulators with a scientific resource allocation tool and decision basis based on the auction theory, and confirms the substantial potential of mechanism design to address complex airspace resource management problems.