The invention discloses a protocol inventory matching and optimal allocation method. According to the method, protocol inventory matching is solved based on a branch definition algorithm, and balanced matching of a region and a schedule, considered by a protocol inventory, is finished; and the method comprises protocol inventory modeling and establishment of a protocol inventory intelligent algorithm. According to the method disclosed by the invention, the balanced matching of the region and the schedule, considered by the protocol inventory, is finished by the method for solving the protocol inventory matching problem based on the branch definition algorithm; the balance of the region and the schedule can be considered; a calculation result is accurate and a purchasing period of a supply chain is short; and meanwhile, an executing result can be comprehensively analyzed and evaluated, deviation overflow in a decision-making process can be explained, and the requirements are met.