The aim of this study is to clarify the calculation of economic compensation within the urban emergency transportation capacity requisition mechanism during public health emergencies. This paper establishes an emergency capacity pool for social vehicles at three levels—city, county, and community. The pool primarily targets third-party logistics enterprises, supported by temporary transportation capacity from social sources. Considering requisition expenses, financial losses, economic incentives, and other relevant factors, a mathematical model is proposed using cost analysis to determine compensation for transportation capacity requisition. A cost correction coefficient is introduced to calculate the compensation standard for urban emergency capacity requisition. Finally, the model’s validity is verified through a case study of an urban public health emergency. The results indicate that applying a fixed cost modification coefficient of 1.04:1:1.92 and a variable cost modification coefficient of 1.06:1:3.50 for the three types of vehicles can standardize requisition compensation calculations. This approach provides an objective, scientific benchmark for market reference and reduces discrepancies in compensation calculations between the government and enterprises during emergency requisitions. This paper also establishes theoretical foundations for standardizing regulations on compensation for urban emergency capacity requisitions.