Objective To systematically review the efficacy and safety of polyethylene glycol and sodium phosphate in bowel preparation of capsule endoscopy. Methods We searched CNKI, CBM, WanFang Data, PubMed, EMbase, and The Cochrane Library (Issue 6, 2016) up to June 2016, to collect randomized controlled trials (RCTs) about polyethylene glycol and sodium phosphate in bowel preparation of capsule endoscopy. Two reviewers independently screened literatures, extracted data and assessed the risk of bias of included studies, and then meta-analysis was performed by using RevMan 5.0 software. Results A total of six RCTs involving 531 patients were included. The results of meta-analysis showed that: compared with the sodium phosphate solution group, the polyethylene glycol solution group had poor intestinal cleansing effect (OR=0.43, 95%CI 0.21 to 0.88,P=0.02), higher incidence of adverse reaction (OR=3.20, 95%CI 1.13 to 9.06,P=0.03); but shorter gastric retention time (OR=–11.61, 95%CI –13.71 to –9.51,P<0.000 01) and residence time in the small intestine (OR=–4.17, 95%CI –7.74 to –0.60,P=0.02). Conclusion The efficacy of oral polyethylene glycol is poor in cleaning effect and adverse reaction than sodium phosphate solution, but better in the digestive tract residence time for capsule endoscopy. Due to the limited quality and quantity of included studies, the above conclusion is still needed to be proved by more high-quality studies.