Recently, a novel reference-frame-independent measurement-device-independent quantum key distribution protocol was proposed, which can remove all detector side channels as well as tolerate unknown and slow variance of reference frame without active alignment. In this paper, we propose a new tomographic method to estimate the key rate in that protocol. We estimate the key rate using conventional method and tomographic method respectively and compare the two methods by numerical simulation. The numerical simulation results show that tomographic approach is equivalent to the conventional approach, which can be used as an alternative method. Recently, a novel reference-frame-independent measurement-device-independent quantum key distribution protocol was proposed, which can remove all detector side channels as well as tolerate unknown and slow variance of reference frame without active alignment. In this paper, we propose a new tomographic method to estimate the key rate in that protocol. We estimate the key rate using conventional method and tomographic method respectively and compare the two methods by numerical simulation. The numerical simulation results show that tomographic approach is equivalent to the conventional approach, which can be used as an alternative method