An algorithm of inverting atmospheric turbulence phase screen based on non-uniform sampling power spectrum is analyzed. Parallel progressing can be realized in the algorithm, and a graphics processing unit (GPU) is introduced. The speed of phase screen simulation can be effectively improved without affecting the simulation precision. Atmospheric turbulence phase screen is generated based on GPU technique while the Kolmogorov power spectrum is used. The simulation accuracy, simulation speed and error of phase screen are statistically analyzed and compared with theoretical values. Results show that the atmospheric turbulence phase screen simulated by GPU technique is consistent with the theoretical value, and has high simulation speed and high simulation precision. The generation speed of atmospheric turbulence phase screen is greatly improved.