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Drought is an important factor limiting the growth and development of rice and thereby seriously affects rice yield. The problem may be effectively solved by dissecting the drought-resistance mechanism of rice, creating excellent drought-resistant germplasm, and mining new drought-resistant genes. In this study, 305 accessions (189 <i>Xian</i>, 104 <i>Geng</i>, 5 <i>Aus</i>, and 7 <i>Basmati</i>) were used to identify drought-related phenotypes such as grain yield per plant (GYP), grain number per panicle (GNP), panicle number per plant (PNP), and plant height (PH) under two-year drought stress. The 2017 GYP and 2018 GNP were <i>Xian</i> max, 2018 GYP, 2017 GNP, 2017 and 2018 PNP, and 2018 PH were <i>Basmati</i> max, and only the 2017 PH was <i>Geng</i> max. The population genetic diversity and population structure were analyzed by combining 404,388 single nucleotide polymorphism (SNP) markers distributed on 12 chromosomes. A total of 42 QTLs with significant correlations was identified, among which 10 were adjacent to the loci reported to be associated with drought resistance. Four candidate genes, <i>LOC_Os03g48890</i>, <i>LOC_Os04g35114</i>, <i>LOC_Os11g45924</i>, and <i>LOC_Os06g38950</i>, were identified by functional annotation and haplotype analysis. The R² of <i>qGYP3.1</i> was 11.53%, the R² of <i>qGNP4.2</i> was 12.09%, the R² of <i>qPNP11.1</i> was 10.01%, and the R² of <i>qPH6.1</i> was 13.06%. The results have an important theoretical significance and practical application value for the improvement of drought resistance in rice.