The navigation pseudo random long code period is 7 days generally. When the time uncertainty is ±1 s and the code rate is 10.23 MHz, the chips needed to search are up to 20 460 000. So it is difficult to realize acquisition in short time with common methods. By increasing the consumption of hardware resource and reducing the coherent integration time, the acquisition speed will be increased. Nevertheless this will lead to the decrease of the acquisition sensitivity due to the limited hardware resources. In order to realize the acquisition quickly without affecting the acquisition sensitivity with the limited hardware resources, the two-dimensional parallel search method based on Fast Fourier Transform (FFT) is presented. By comparing with the methods of code phase parallel searching based on FFT and matched filtering +FFT in three aspects: acquisiton time, sensitivity, and hardware resources, the proposed algorithm is demonstrated to have advantages of fast acquisition speed, high sensitivity, and rational use of the hardware resources in the long code acquisition.