The use of acoustophoretic separation devices provides a feasible means in biomedical diagnostics for label-free separation of diseased cells. Separation via acoustophoresis, however, has been restricted mainly to size contrast. Thermally-assisted acoustophoresis, as a newly-developed approach, integrates acoustic and thermal actuators on the same platform, enabling a stiffness-based separation when adjusted properly. Using this method, we have demonstrated the possibility of separating cell-mimicking liposomes based on their membrane stiffness. In a temperature-tuned microchannel with an overlaid ultrasonic standing wave, the acoustic contrast factor of a liposome is mainly determined according to its compressibility compared to that of medium. The sign of this factor was observed to flip to a negative value at a specific temperature, unique to the composition of the liposome. This sign switch was hypothesized to be due to the thermotropic phase transitions in the liposome’s membrane upon which an apparent effect on the compressibility is experienced by the liposome. By choosing the midpoint of the existing temperature window for two different compositions, within which liposomes were mechanically distinct enough to become differentiable in the acoustic radiation field, we examined the separation efficiency under different flow rate conditions.