Introduction Minimally invasive lung surgery (MILS) gradually became the primary surgical therapy for lung cancer, which remains the leading cause of cancer death. Adequate muscle relaxation by deep neuromuscular block (NMB) is particularly necessary for MILS to provide a satisfactory surgical field. However, deep NMB for MILS remains controversial, as one-lung ventilation may provide an acceptable surgical field. Then, we will perform a protocol for a systematic review and meta-analysis to identify the efficacy of deep NMB for MILS. Methods and analysis We will search the PubMed, Cochrane Library, Embase, Ovid Medline, Web of Science, Chinese BioMedical Literature, China National Knowledge Infrastructure, VIP and Wanfang databases from inception to March 2022 to identify randomised controlled trials of adult participants undergoing MILS with deep NMB. Studies published in English or Chinese will be considered. The primary outcome will be the surgical conditions according to the surgeon's perspective. Secondary outcomes will be the incidence of perioperative events and perioperative mortality. Heterogeneity will be assessed by the chi(2) test and I-2 statistic. Data will be synthesised by both a fixed-effect and a random-effects meta-analysis, with an intention to present the random-effects result if there is no indication of funnel plot asymmetry. Otherwise, metaregression will be used. The Cochrane risk-of-bias tool, trial sequential analysis and Grading of Recommendations Assessment, Development and Evaluation will be used to assess the evidence quality and control the risks of random errors. Funnel plots and Egger's regression test will be used to assess publication bias. Ethics and dissemination Ethical approval was not required for this systematic review protocol. The results will be disseminated through peer-reviewed publications. PROSPERO registration number CRD42021254016.