To overcome the unbalanced signal-to-noise ratio (SNR) among data-carrying subcarriers (SCs) induced by the imperfect frequency response of optoelectronic devices and various interferences, a channel-independent partial data-carrying SCs precoding (PDSP) method based on orthogonal circular matrix transform (OCT) is proposed and experimentally investigated in an intra-symbol frequency average (ISFA)-enabled discrete multi-tone (DMT) visible light communication (VLC) system. After transmission over 1.9 m free space, at the optimal bias current of 100 mA, the experimental results show that the bit error ratio (BER) performance can be improved by up to an order of magnitude with conventional full data-carrying SCs precoding (FDSP) and PDSP scheme, compared to that without a precoding scheme. Moreover, the BER performance can further be enhanced when the ISFA algorithm with optimal taps is employed. Compared with the FDSP scheme, the proposed PDSP scheme owns a similar BER performance and a significant reduction in required multiplication and addition operations, and it may be a good option to efficiently combat the unbalanced impairments of DMT-VLC transmission systems.