This study provides a new perspective on the drone delivery problems (DDP) by conceptualizing the vertical space in multiple flight levels. The main advantage of drone delivery is efficiency in utilizing free three-dimension aerial space, enabling numerous travels at multiple flight levels. However, the operational efficiency tradeoff exists according to the flight level, particularly in metropolitan cities with countless skyscrapers. Operation on the upper level requires less detour on horizontal movement, but it needs more time on the vertical movement of drones to reach the upper level. This study introduces a novel DDP by dividing the vertical airspace into multiple flight levels, thereby providing an opportunity to increase overall delivery efficiency based on realistic constraints faced by cities. We formulate this problem into a mathematical model and suggest a new supervised machine learning approach called SPML (Sequential Prediction Machine Learning). The SPML has three phases. In the first phase, customers are sequenced by priority. The second phase uses a supervised machine learning model trained by the data collected from solving the mixed-integer linear programming (MILP) model to assign customers to the depot. The third phase is distributing jobs to drones by using dynamic programming.