Aiming at the problem of inter-cell interference in indoor visible light communication(VLC) systems, a resource allocation algorithm for multi-cell coordinated multiple-input multiple-output(MIMO) orthogonal frequency division multiple access (OFDMA) VLC system with joint light source layout is proposed. First, without affecting the lighting, by optimizing the light source layout, the cell interference is limited to the coverage of two LEDs. Then, cooperative MIMO technology is introduced to take user fairness as the optimization goal. Finally, the resource allocation performance of MIMO OFDMA VLC system for two cooperative modes(SMP) and repetition coding(RC) is simulated. The simulation results show that the performance of the MIMO OFDMA VLC system of the two cooperative modes is better than that of the single-input single-output(SISO) OFDMA VLC system. The VLC system based on RC mode is robust to channel correlation, and its transmission rate is about 1.2 times that of the SISO OFDMA VLC system. When the channel matrix condition number is lower than six, the VLC system based on the SMP mode has better performance because of the larger multiplexing gain. When the channel matrix condition number is equal to two, the data transmission rate of the VLC system is approximately that of the SISO OFDMA VLC system 1.32 times.