An apparatus and a method of synchronizing and interpolating axes of a multi-system are provide. According to the number M of operating systems, the apparatus analyzes a multi-axis process program of N axes to generate M system process programs, wherein, N≧M≧2. A synchronous code is added to the M system process programs. According to the specifications of the operating systems, a delay time compensation program is added to the M system process programs to ensure the synchronization of the systems therebetween. The characteristics of the controllers and the servos of the operation systems are adjusted to unify the characteristics of the systems. The M system process programs are outputted to the operating systems correspondingly.