Aiming at the high precision NCO realization demand of aerospace TT&C system, a high precision NCO realization method based on GPU is designed by utilizing the high flexibility and high efficiency parallel data processing capability of GPU. Aiming at the common problem of large cumulative error in the phase accumulation operation of floating point numbers in NCO calculation, a single precision phase accumulation comprehensive compensation algorithm based on Fast2Sum algorithm and 2Sum algorithm is designed by using the Error-Free transformation technology, and a phase accumulation summation operator is designed for NCO system. Finally, the design method is verified based on GPU platform. The experimental results show that the design method can control the phase accumulation error of GPU-based NCO system at 1×10–5 rad.