In cooperative MIMO relay systems, when amplify-and-forward (AF) mode is used, the equivalent channel from source station (SS) to destination station (DS) can be seen as a simple MIMO channel. When singular value decomposition (SVD) based precoding is used in the system, the equivalent channel can be decomposed into several parallel non-interfering subchannels. It is showed that some of the singular values of the subchannels can be very small and the performance of the whole system is limited by the subchannels with the lower gains. Thus it is important to decide how many subchannels should be used to maximize the system performance. In this paper, we propose that half of the subchannels with higher singular values should be used, with the joint consideration of data rate and bit error rate (BER). The simulation shows that when the data rate is fixed, the proposed methods can achieve the optimal BER performance.