An improved blind phase noise compensation algorithm, two-stage projection histogram (PH) algorithm, is proposed. Firstly, we use a series of uniformly distributed test phases to rotate the phase of the received signal, and project the received signal onto the real axis to obtain the projected histogram; secondly, we count the number of constellation points near the projection center and take the test phase with the largest number as the coarse phase shift value; thirdly, we consider coarse phase shift value as the center, take a certain number of test phases uniformly, repeat the estimation steps of the one-stage PH, and obtain the accurate phase shift value for phase compensation. The performance of the proposed algorithm is experimentally verified in the coherent optical orthogonal frequency division multiplexing passive optical network (CO-OFDM-PON) system based on optical comb. The results show that the proposed algorithm has a good compensation effect on the common phase noise of 10×8 Gbit/s CO-OFDM system, and the bit error rate (BER) is reduced by at least two orders of magnitude. Compared with the one-stage PH algorithm, the proposed algorithm need only 1/4 number of test phases, which greatly reduces the complexity of the system and can be used to common phase noise compensation for CO-OFDM systems.