In this paper, wireless multiple-input multiple-output (MIMO) ultraviolet communication is combined with a linear water-filling algorithm. First, a wireless non-line-of-sight (NLOS) MIMO ultraviolet communication model based on the linear water-filling algorithm is established and its channel capacity model is derived. Then, the equal power allocation algorithm and the linear water-filling algorithm are used for power allocation at the signal transmitter. The influences of these two methods on the channel capacity of the wireless NLOS MIMO ultraviolet communication system are studied, and simulation analysis and verification are conducted. The simulation results show that at the same signal-to-noise ratio (SNR), when the transmitting and receiving antennas are asymmetrical, the channel capacity of the communication system adopting the linear water-filling algorithm in wireless NLOS MIMO communication is significantly higher than that of the system employing the equal power allocation algorithm. When the transmitting and receiving antennas are symmetrical and the SNR is small, the water-filling algorithm can significantly improve the channel capacity. When the SNR increases to a certain value, the channel capacity of power allocation obtained via the water-filling algorithm is close to that obtained via the equal power allocation algorithm.