Complicated monochorionic twin pregnancies are often associated with high perinatal morbidity and mortality, some of which are severe enough to require a gestational reduction surgery to improve fetal survival and reduce disabilities. While radiofrequency ablation is currently the most commonly used procedure with higher fetal survival and fewer maternal and fetal complications compared with other surgical methods, the therapeutic effect of microwave ablation (MWA) is reported to be better, presumably due to the higher thermal effect and fewer restrictions. Currently there is limited evidence to prove the feasibility of MWA for selective reduction. The aim of this pilot study is to explore the feasibility, efficacy and safety of MWA reduction for severe complicated monochorionic pregnancies and may provide evidence for using the MWA in intrauterine surgeries extensively. This is a study protocol for a parallel-design pilot randomised controlled trial. 60 eligible patients with severe complicated monochorionic pregnancies will be randomised in a ratio of 1:1 to MWA group and radiofrequency group. Patients will be followed up until 6 months of age of the retained fetal. The primary analysis will compare the rates of neonatal survival at 28 days to evaluate the effect of MWA. The study will also evaluate the safety profile of MWA including the occurrence of postoperative adverse events and maternal and fetal complications. Additional secondary outcomes to be explored include the condition of neonatal asphyxia and the growth of surviving fetus at 6 months. Outcomes will be analysed by both a frequentist and the Bayesian statistical approach. This study was approved by the ethical review committee of the Peking University Third Hospital (Beijing, China). The results of this study will be published in peer-reviewed scientific journals and presented at relevant academic conferences. NCT04014452; Pre-results. © Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.