Using the mixed fatty acids (MFA) produced by waste cooking oil as flotation collectors directly, the flotation effect is usually not satisfactory, especially at lower temperature, which may be due to the presence of large amounts of saturated fatty acids. In this study, waste cooking oil was separated into saturated fatty acids (SFA) and unsaturated fatty acids (UFA). The separation mechanism was studied by molecular simulation based on quantum and molecular mechanics. SFA and UFA were analyzed by iodine value, melting point measurement and Fourier transform infrared (FT-IR) spectroscopy to check the result of the separation. The micro-flotation and bench-scale flotation tests were performed to investigate the flotation differences between SFA and UFA. The results showed that the poor flotation performance of waste cooking oil was due to the large amount of SFA in presence. If the SFA was separated out, the TFe grade and recovery of the flotation concentrates would be increased by 4.09 and 2.70 percentage points, respectively and the SiO2 grade would be 4.03 percentage points lower at the same time. This study would provide technical supports and theoretical guidance for the waste cooking oil application in the field of mineral processing.