Thermal strain imaging (TSI) uses echo shifts in ultrasonic B-scan images to estimate changes in temperature which is of great values for thermotherapies. However, for in vivo applications, it is difficult to overcome the artifacts and errors arising from physiological motions. Here, a respiration separated TSI (RS-TSI) method is proposed, which can be considered as carrying out TSI in each of the exhalation and inhalation phases and then combining the results. Normalized cross correlation (NXcorr) coefficient between RF images along the timeline are used to extract the respiratory frequency, after which reference frames are selected to identify the exhalation and inhalation phases, and the two phases are divided quasi-periodically. RF images belonging to both phases are selected by applying NXcorr thresholds, and motion compensation together with a second frame selection helps to obtain two finely matched image sequences. After TSI calculations for each phase, the two processes are merged into one through extrapolation and interphase averaging. Compared to TSI based on dynamic frame selection (DFS), RS-TSI ensures that frames are selected during both the exhalation and inhalation phases while setting the frame selection range according to the respiratory frequency helps to improve motion compensation. The temporal intervals of TSI output are approximately half that employing DFS.