The invention discloses an automatic unmanned plane express delivery shortest path program method. The address information of each to-be-delivered express is scanned through scanning equipment, all target sites of a present delivery task are determined, and the shortest path starting from an express distribution center, passing by all the target sites and finally returning back to the express distribution center is programmed. An initialization algorithm is firstly provided, a population including a series of molecules is generated, and each molecule represents a feasible path satisfying the delivery task; four corresponding chemical reaction sub algorithms are further provided, including a decomposition algorithm, a synthesis algorithm, a local search algorithm and a greedy search algorithm, iteration is carried out according to relevant rules, the molecule population is made to realize continuous evolution till iteration termination conditions are satisfied, a molecule of the population having the smallest potential energy is found out, and the optimal path is programmed. The method is advantaged in that on the condition that the delivery task of all the target express sites is accomplished, the total flight path of the unmanned plane is the shortest, the total consumption time is the shortest, consumption energy is effectively reduced, and express delivery efficiency is improved.