This paper applies the repetition index scheme (RIS) to the channel identifi-cation of cyclic prefixed (CP) multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) systems with virtual carriers (VCs) in the environment of the number of receive antennas being no less than that of transmit antennas. The VCs will cause a rank deficiency problem in computing the subspace information. With the subcarrier mapping matrix, the received signal is sim-plified to remove the rank deficiency. We use the RIS scheme to generate many times of equivalent symbols so the channel identifica-tion can converge with few received OFDM blocks. The RIS scheme will convert the white noise into non-white noise. With the Cholesky factorization, a noise whitening technique is developed to t the non-white noise back to white noise. We further analyze the necessary conditions of identifiability of channel estima-tion. Simulations are performed to show the superiority of the proposed method.