Wireless optical communication is a crucial direction for improving the data transmission rate in underwater environments. In order to improve the communication performance over the water channel, this paper studies underwater wireless optical communication (UWOC) employing polarization multiplexing modulation and photon counting detection. The improvements in bit error rates and communication capacities are analyzed theoretically by constructing the communication model of polarization multiplexing modulation UWOC based on photon counting. Under specific conditions, the polarization maintenance characteristics of photons over water channels are demonstrated by measuring the Mueller matrix, the fidelity of quantum states, depolarization ratio, and calculating the ratios of ballistic photons. Based on these results, by designing and developing the experimental system of UWOC with the polarization multiplexing modulation and photon counting detection, the data transmission rates of 14.58Mbps and 7.29Mbps are realized over a water channel of 92 m by using polarization on-off keying multiplexing modulation and polarization 2-pulse-position multiplexing modulation, respectively.