This paper focuses on the modal aliasing resulted from the abnormal signal in practical applications of Empirical Mode Decomposition (EMD). A method based on two-scale proportional criterion and local EMD is proposed. First, an analysis is made to the impact of the abnormal signals on EMD algorithm, and the two-scale criterion combining the time characteristic scale with the extreme difference is established. The time domain location of the abnormal signal is determined by the criterion, and the abnormal signal is then separated from inherent signal by means of local EMD during the period. Numerical simulation results and comparative analysis show that the method can settle the problem of modal aliasing caused by abnormal signal more effectively compared with conventional methods.