The control method of Multiple Input Multiple Output sine-on-random (SoR) vibration test is systematically discussed in the paper. It is pointed out that the accurate separation of mixed signals, which consist of sine and random signals, is the key factor to improve the control precision. A new separation method called Uncorrelated Integration is proposed out of its filtering characteristics to identify the amplitudes or phases of sine signals in the time domain, and the method can avoid the problem of energy leakage in frequency domain. The formula that sine signals of certain frequency separated from the mixed signals is derived in detail, and numerical calculation shows that the identification accuracy is 0.44%. A two input two output vibration system model is established. The random signals and sine signals are controlled by proportional RMS updating algorithm and amplitude updating algorithm respectively. The power spectrum density (PSD) of random signal is limited to ?3 dB of the reference PSD, and the amplitudes of sine signals are limited to ?10% of the reference value. The results show that the method proposed can meet the engineering demand.