At present, there is an increasing awareness of some three-orthogonal-basis quantum key distribution protocols, such as, the reference-frame-independent(RFI) protocol and the six-state protocol. For secure key rate estimations of these protocols, there are two methods: one is the conventional approach, and another is the tomographic approach. However, a comparison between these two methods has not been given yet. In this work, with the general model of rotation channel, we estimate the key rate using conventional and tomographic methods respectively. Results show that conventional estimation approach in RFI protocol is equivalent to tomographic approach only in the case of that one of three orthogonal bases is always aligned. In other cases, tomographic approach performs much better than the respective conventional approaches of the RFI protocol and the six-state protocol. Furthermore, based on the experimental data,we illustrate the deep connections between tomography and conventional RFI approach representations. There are an increasing awareness of some three-orthogonal-basis quantum key distribution protocols, such as, the reference-frame-independent (RFI) protocol and the six-state protocol. For secure key rate estimations of these protocols, there However, a comparison between these two methods has not been given yet. In this work, with the general model of rotation channel, we estimate the key rate using conventional and tomographic methods respectively. Results show that conventional estimation approach in RFI protocol is equivalent to tomographic approach only in the case of that one of three orthogonal bases is always aligned. In other cases, tomographic approach performs much better than the respective conventional approaches of the RFI protocol and the six-state protocol. Further, based on the experimental data, we illustrate the deep connections between tomography and conventional RFI approach representationsations.