A direct sequence spread spectrum (DSSS) signal is commonly used in inter-satellite link (ISL) in navigation constellation; however, acquisition is a challenging task because of large-scale relative movement between satellites. In general, a signal search (carrier frequency and code phase) is implemented using two-dimensional partitioned fast Fourier transforms (FFTs), which is limited by the memory of the processor. Nevertheless, the carrier's continuity is damaged by the circular shift. Noncoherent integration is performed to circumvent this problem. However, the acquisition sensitivity will be reduced because of the square loss. In this paper, we analyze the processing flow of traditional noncoherent integration method and the new presented coherent integration method with compensation. Besides, the comparison of computation cost between the new approach and the conventional method is done. Numerical results show that the coherent method can improve the sensitivity of acquiring weak signals and save about 60% computation cost as well.