In the power line communication system (PLC), large amount of noise exist between transmitter and receiver which seriously affects the reliability of the signal transmission. This paper presents a noise mitigation method based on time-frequency peak filtering (TFPF). However, there is a large restriction to TFPF by the selection of window length. In order to obtain the good trade-off between noise suppression and amplitude preservation, this paper adopts EMD method to assist TFPF. It utilizes the decomposition characteristic of EMD which can decompose a signal to a series of intrinsic mode functions (IMFs) from high frequency to low frequency and select different window length for these modes. Numerical experiments show that the EMD-TFPF method can effectively eliminate the power line communication system noise, reduce the Bit Error Rate (BER) and improve the quality of communication system. Moreover, it can make a better tradeoff between noise suppression and amplitude preservation.