The invention provides a multi-joint measuring arm based digital measuring system and method for geometric characteristics of a guided missile. The measuring system comprises a guided missile supporting platform, a multi-joint measuring arm, measuring brackets and a data acquiring processing system, wherein the guided missile supporting platform is a platform capable of providing all missile support, so that the missile is guaranteed to meet requirements of a measuring state; the multi-joint measuring arm is a market mature product, has arm length greater than 3.5 meters, has measuring precision not smaller than 0.5 mm, and is used for acquiring coordinate values of each measuring point on the missile body; the measuring brackets are supporting structures of the multi-joint measuring arm,are fixedly arranged on the supporting platform, and are arranged front and rear separately; and the data acquiring system consists of a computer, a data line and data processing software, and is usedfor acquiring and processing the measured data of the measuring arm to form a measured report form. According to the multi-joint measuring arm based digital measuring system and the method provided by the invention, process flow is optimized, digital measuring is realized, and turnover, among stations, of the guided missile is reduced while efficiency is improved.