Compared with the composite shaft double detection system, a single composite shaft detection system has the advantages of simple structure, low cost and high reliability, but its decoupling control complexity is a great technical challenge. In the laser countermeasure field for high precision tracking-pointing system, the complexity of the decoupling control is mainly manifested at two aspects of the coarse fine matching bandwidth of decoupling and coarse fine pointing alignment. Master of shaft alignment relationship transform problem is one of the core technology breakthrough difficulties, it’s accuracy determines whether the real-time tracking-pointing system error correction is optimal or not, which directly affect the tracking-pointing accuracy. Two common single detection methods are used as examples to illustrate the composition principle of the single detection compound shaft system and the importance of the pointing alignment. And the method of combining the least square fitting calculation with the verification of the special instrument is put forward to determine the high precision alignment parameters. High precision tracking-pointing can be achieved by integrating the decoupling matrix with the controller and implementing coarse fine decoupling control in real time. Field experimental testing and verification results show that the accuracy of this method can meet the system requirements. The fine tracking of the single detection composite shaft system is superior to 2 arc seconds. And the single composite shaft detection system achieving good tracking-pointing effect is verified.