Objective To systematically compare the effect of internal therapy of traditional Chinese medicine（TCM）with prokinetic agents on functional dyspepsia(FD). Methods Databases of CNKI， CBM， Wan Fang， VIP， PubMed were retrieved，and the randomized-controlled trials（RCTS） which compared the effect of internal therapy of TCM with prokinetic agents on FD were collected. Improved Jadad Quality Scale was used for quality assessment. Meta-analysis was performed with RevMan5.3 software. Results A total of 28 RCTS were included 2 143 patients， including 1 074 patients in the experimental group and 1069 patients in the control group. Meta-analysis result： Camparing with the control group， the experimental group had advantages in increasing the total effective rate[RR=1.25，95%CI(1.20， 1.30)， P<0.000 01]，improving the symptoms of TCM[MD=-3.29， 95%CI(-4.17, -1.87)， P<0.000 01] and western medicine(P<0.000 01)， but not advantages in reducing adverse events[RR=0.71， 95%CI(0.35, 1.43)， P=0.33]. Conclusion Internal therapy of TCM were more effective than prokinetic agents for the treatment of FD， but with equivalent safety.