Chemical exchange saturation transfer (CEST), arising from the generally mobile groups, and magnetization transfer (MT) contrast arising from immobile protons, have enjoyed wide popularity recently in MRI applications. It is often difficult to separate genuine CEST signatures from MT effects, which are asymmetric with respect to the water resonance. A two-pool model for magnetization transfer (MT) is established fully based on Provotorov’s theory of saturation, and then extended to the situation of simultaneous two-frequency rf irradiation. Numerical simulations and experimental results demonstrate that two-frequency rf irradiation can flatten out MT asymmetry when both frequency components lie within the spectrum of an MT pool. Based on this result, we propose a strategy to isolate chemical exchange saturation transfer (CEST) contrast from MT asymmetry contrast by using the two-frequency rf irradiation technique.