To reduce distribution risk and improve the efficiency of medical materials delivery under major public health emergencies, this paper introduces a drone routing problem with time windows. A mixed-integer programming model is formulated considering contactless delivery, total travel time, and customer service time windows. Utilizing Dantzig–Wolfe decomposition, the proposed optimization model is converted into a path-based master problem and a pricing subproblem based on an elementary shortest path problem with resource constraints. We embed the pulse algorithm into a column generation framework to solve the proposed model. The effectiveness of the model and algorithm is verified by addressing different scales of Solomon datasets. A case study on COVID-19 illustrates the application of the proposed model and algorithm in practice. We also perform a sensitivity analysis on the drone capacity that may affect the total distribution time. The experimental results enrich the research related to vehicle routing problem models and algorithms under major public health emergencies and provide optimized relief distribution solutions for decision-makers of emergency logistics.