As an application of the direct sequence spread spectrum (SS) communication system, there is an M-ary bi-orthogonal SS communication system. In its system, several spreading sequences (bi-orthogonal sequences) are used in a code shift keying basis. Hence, design of the spreading code synchronization system has been an issue in the M-ary bi-orthogonal SS systems. In this paper, the authors focus on a code tracking system using a differential detector and a Delay Lock Loop (DLL). They investigate a tracking performance of their code tracking system by theoretical analysis. In addition, a multi-stage interference canceler is applied to the M-ary bi-orthogonal SS system. As the result, it is shown that the tracking performance of the theoretical analysis is almost the same as that of computer simulations in a multi-user environment. It is also shown that the multi-stage interference canceler is effective in improvement of the BER performance.