The rise of youth development cities stems from the intersection of common urban development issues in China and the unique development challenges faced by the youth. The aggregation or dispersion of urban spatial structures directly influences the concentration of young talent and the efficiency of innovative element allocation. This paper empirically analyzes the impact of the spatial structure of youth development cities on the misallocation of innovative elements using LandScan population distribution data from 2008 to 2021. The study finds that the degree of spatial dispersion in youth development cities is on the left side of the "U-shaped" structure of innovative element misallocation, with a further trend towards aggregation. The dynamic flow mechanism of elements shows that the spatial structure of youth development cities alleviates the misallocation of innovative elements through the bidirectional flow of innovative capital and personnel, especially benefiting surrounding cities through the flow of innovative personnel. The static mechanism indicates that the innovative allocation environment of elements optimizes resource allocation by mitigating the misallocation of innovative capital under the aggregation trend of youth development cities. The study supports the adoption of a reasonable spatial dispersion strategy in the planning of youth development cities to optimize the allocation of innovative elements and proposes corresponding policy recommendations.