Favorable agronomic traits are important to improve productivity of popcorn. In this study, a recombinant inbred line(RIL) population consisting of 258 lines was evaluated to identify quantitative trait loci(QTLs) for nine agronomic traits(plant height, ear height, top height(plant height subtracted ear height), top height/plant height, number of leaves above the top ear, leaf area, stalk diameter, number of tassel branches and the length of tassel) under three environments. Meta-analysis was conducted then to integrate QTLs identified across three generations(RIL, F2:3 and BC2F2) developed from the same crosses. In total, 179 QTLs and 36 meta-QTLs(m QTL) were identified. The percentage of phenotypic variation(R2) explained by any single QTL varied from 3.86 to 28.4%, and 24 QTLs with contributions over 15%. Nine common QTLs located in the same or similar chromosome regions were detected across three generations. Five meta-QTLs were identified including QTLs in three independent studies. Seven important m QTLs were composed of 11–26 QTLs for 4–7 traits, respectively. Only 11 m QTLs were commonly identified in the same or similar chromosome regions across agronomic traits, popping characteristics(popping fold, popping volume and popping rate) and grain yield components(ear weight per plant, grain weight per plant, 100-grain weight, ear length, kernel number per row, ear diameter, row number per ear and kernel ratio) by meta-QTL analysis. In conclusion, we identified a list of QTLs, some of which with much higher contributions to agronomic traits should be valuable for further study in improving both popping characteristics and grain yield components in popcorn. Favorable agronomic traits are important to improve productivity of popcorn. In this study, a recombinant inbred line (RIL) population consisting of 258 lines was evaluated to identify quantitative trait loci (QTLs) for nine agronomic traits (plant height, ear height, top height (plant height subtracted ear height), top height / plant height, number of leaves above the top ear, leaf area, stalk diameter, number of tassel branches and the length of tassel) under three environments. Meta-analysis was conducted then to integrate QTLs identified across three generations (RIL, F2: 3 and BC2F2) developed from the same crosses. In total, 179 QTLs and 36 meta-QTLs (m QTLs) were identified. The percentage of phenotypic variation varied from 3.86 to 28.4%, and 24 QTLs with contributions over 15%. Nine common QTLs located in the same or similar chromosomes were detected across three generations. Five meta-QTLs were identified including QTLs in three independent studie s. Seven important m QTLs were composed of 11-26 QTLs for 4-7 traits, respectively. Only 11 m QTLs were commonly identified in the same or similar chromosome regions across agronomic traits, popping characteristics (popping fold, popping volume and popping rate ) and grain yield components (ear weight per plant, grain weight per plant, 100-grain weight, ear length, kernel number per row, ear diameter, row number per ear and kernel ratio) by meta-QTL analysis. identified a list of QTLs, some of which with much higher contributions to agronomic traits should be valuable for further study in improving both popping characteristics and grain yield components in popcorn.