The invention relates to a flight plan vertical route programming method and system, and belongs to the technical field of flight management. The method comprises the following steps: carrying out optimal storage on basic flight performance data in each of the flight stage, the climbing stage, the cruise stage, the descending stage and the landing stage of an airplane, published by an airplane developer or a production department in an airborne performance database form; defining and describing the vertical route information in each of the flight stage, the climbing stage, the cruise stage, the descending stage and the landing stage based on the optical storage; and conveniently storing the basic vertical navigation route information in an airborne state, designing a complete military and civilian plan vertical route information structure based on the basic vertical navigation route information in an airborne state, and programming a flow to form a military and civilian flight plan vertical route. The logic relationship among all above information structures is close, no redundancy appears among pieces of information, the information storage amount is small, and the system, can be conveniently stored or unloaded, and can be used for ground or other airborne devices.