Introduction As hemostasis is a complex process that bleeding can be difficult to control, higher requirements are needed for spinal surgeons in intraoperative hemostasis. Floseal and Surgiflo are two common thrombin-based flowable hemostatic agents. Nevertheless, Floseal or Surgiflo has not been universally recommended by the current guidelines of preoperative hemostatic management in spine surgery due to lack of relative systematic evidence-based medical evidence. Moreover, adverse effects of novel absorbable hemostatic biomaterial may be poorly reported and inconsistently described. Meanwhile, there is currently no systematic review and meta-analyses available which sum up the existing evidence. Our study aims to explore the efficacy and safety of thrombin-based flowable hemostatic agents in spine surgery, and to provide corresponding evidence-based medical evidence. Methods and analysis Our study will conduct a systematic review and meta-analysis to explore the efficacy and safety of thrombin-based flowable hemostatic agents in spine surgery, based on Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol (PRISMA-P). Two authors will retrieve the relevant articles using the eight databases (PubMed, Scopus, Embase, Cochrane Library, Web of Science, CNKI, Wanfang and CBM) from inception to 16st Aug, 2022. Three authors will screen citation titles and abstracts and evaluated full-text of each potentially relevant citation, and then extract the data using a data extraction form. Any discrepancies in decisions between reviewers will be resolved through discussion. All included studies will be evaluated for quality and risk of bias according to the Cochrane guidelines. A subgroup analysis and a sensitivity analysis will be used to find the main source of between-study heterogeneity. All data analysis will be performed using RevMan v.5.3 Software provided by the Cochrane Collaboration.