The long pseudo-noise codes have the advantages of strong anti-interference capability and high ranging accuracy, which has been used in GPS, Compass and other navigation satellite systems. However, the general acquisition algorithm is no longer applicable in the long codes because the long period property leads to the problem of large computation and high consumption of hardware resource. In order to solve the problems mentioned above, firstly, a long code acquisition algorithm based on parallel phase search which has already been proposed currently is improved by the method of partial averaging, and the simulation results show that the calculated amount is reduced. Then, the employ of multi-correlator and FFT transform in parallel frequency search can not only reduce the computation of acquisition algorithm, but also increase the acquisition speed. In order to receive the long code on the receiver, this paper concentrates on the hardware implementation of long code acquisition algorithm based on multi-correlation parallel frequency search in FPGA. Besides, the operating principle of each module is explained in detail. Through the test on the FPGA board, it is proved that the designed acquisition module can effectively and timely acquire the navigation signal. Moreover, the method of hardware implementation proposed in this paper for long code acquisition has the advantages of small hardware resource consumption and simple implementation structure, which is able to provide a reference for the engineering application of long code acquisition.