A new method for the comparison of the treatment efficacy for specific diseases or conditions between Chinese medicine and Western medicine, which serve the same medical aim but are based on substantially different theoretical systems, was identified. Abiding by the principle of parallel subgroup design of a randomized controlled trial (PSD-RCT), participants were recruited following identical inclusion and exclusion criteria and were randomly allocated into two groups to receive treatment using the respective approaches of Chinese medicine and Western medicine. The Chinese medicine group was divided into subgroups according to the theory of Chinese medicine and the Western medicine group was also divided into subgroups according to the theory of Western medicine. The treatment for each subgroup was well defined in the protocol, including major formulae and principles for individualized modifications. The primary outcome measure was ascertained to be directly related to the patients' status but independent from both theories of Chinese medicine and Western medicine, while the secondary outcomes were represented by the patient-reported outcomes and some laboratory tests commonly accepted by Chinese medicine and Western medicine. Then, taking functional dyspepsia as an example, the authors explain the framework of the PSD-RCT for efficacy comparisons between Chinese medicine and Western medicine, and recommend that the PSD-RCT can be used to compare treatment efficacy for a specific disease or condition between Chinese medicine and Western medicine, and the comparison among subgroups can provide valuable clues for further studies.