Matrix effect (ME) is commonly seen in electrophoretic separation, but this phenomenon lacks any systematic study. Our work aimed to find out the relationship between separation efficiency and current, and then figure out an effective, simple, and economic solution to overcome the negative impact of ME. This present study showed that small amount of NaCl (0.005 mg/mL) in the sample had no impact on the separation but enhanced the sensitivity. However, when concentration of NaCl increased above 0.005 mg/mL, it alleviated the separation efficiency, sensitivity, and migration time. Besides, increasing NaCl concentration resulted in increasing turning point. The study of relationship of current and NaCl concentration indicated that when the TP of a sample is higher than 62.36 A, desalination is necessary. Since the reported desalination methods are either expensive or complicated, we developed a simple and economic method by simply adding 12 times (volume) of chloroform/methanol (2:1, v/v) into the sample. When applied this method to turtle jelly, the number of theoretical plate (N) of 20 amino acids got up to threefold enhancement.