Introduction. Atopic dermatitis (AD) and diarrhea-predominant irritable bowel syndrome (IBS-D) are two recurrent diseases with limited effective treatments. In Chinese Medicine (CM) theory, they may share dampness pattern as the same dominant pathogenesis at a certain stage and, thus, can be treated with the same method. While Chinese herbal formula Huoxiang Zhengqi (HXZQ) has been reported as an effective dampness-resolving therapy for both AD and IBS-D, further high-quality clinical studies are still needed. In addition, HXZQ lacks accurate clinical positioning based on CM patterns. Therefore, we utilize a master protocol design to evaluate HXZQ for dampness pattern simultaneously in AD and IBS-D, with the aim of identifying the pattern-defined population of HXZQ. Methods and Analysis. This master protocol design includes two randomized controlled trials (RCTs) and a real-world observational study. Based on two registry cohorts of AD and IBS-D, patients with dampness pattern will be enrolled in the RCTs to receive either HXZQ oral liquid or a placebo for 4 weeks and then will be followed up for another 4 weeks, while patients with nondampness pattern will constitute the observational study and experience a 12-week follow-up. A total of 678 AD patients and 322 IBS-D patients will be recruited from 14 hospitals in China over a 3-year period. The eczema area and severity index (EASI) and the proportion of responders for adequate relief (AR) are the primary outcomes in AD and IBS-D, respectively. Analysis will be undertaken separately in each substudy, and then an overall analysis combining multiple subgroups will be performed to comprehensively investigate the effect of HXZQ. Discussion. This study will provide high-quality efficacy evidence of HXZQ for AD and IBS-D patients and give an example of postmarketing evaluation for CM products under the pattern dominating different disease research model. The study is registered with ChiCTR1900026700 and ChiCTR1900026837.Copyright © 2021 Qian Huang et al.