In this paper, efficient individual and joint constant amplitude zero auto-correlation (CAZAC) precoding schemes are proposed to improve the performance of an indoor multiple-input multiple-output-orthogonal frequency division multiplexing (MIMO-OFDM)-based visible light communication (VLC) system. By considering the proposed precoding scheme, a 3×3 MIMO-OFDM VLC system with symmetrical and asymmetrical structure is set up, whose peak-to-average-power ratio (PAPR) of transmitted signal, signal-to-noise ratio (SNR), and bit error rate performance are investigated. It is shown that both individual and joint CAZAC precoding schemes can reduce the PAPR of the transmitted signal and make the SNR uniform over data subcarriers, resulting in significant performance improvement compared to the system without precoding. It is demonstrated that there are similar performance improvements for the MIMO-OFDM VLC system using the individual CAZAC precoding and joint CAZAC precoding in a symmetric scenario. At the expense of higher implementation complexity, the joint CAZAC precoding has more performance benefits than the individual CAZAC precoding for the VLC system with asymmetrical MIMO.