Orthogonal frequency division multiplexing with index modulation (OFDM-IM) is an extension of the traditional OFDM modulation scheme. Its key idea is to adopt the activated subcarrier index to carry extra information. In this paper, we propose a new optical multi-input multiple-output (MIMO) visible light communication (VLC) system based on OFDM-IM and generalized light-emitting diode (LED) index modulation (GLIM). The proposed scheme utilizes the subcarrier index selection to improve the system flexibility and adopts the LED index modulation to increase the spectral efficiency, which also avoids the Hermitian symmetry processing. Simulation results show that the proposed scheme achieves better bit error rate (BER) performance than the traditional GLIM scheme. Moreover, the proposed scheme can flexibly select the number of the active subcarriers according to the channel condition and ensure better system performance.