Plant height is an important agronomic trait in rice, usually relating to yield-related traits. Here, a novel rice chromosome segment substitution line Z1377 with increased plant height was identified from recipient Nipponbare and donor Jinhui 35 through selection of both phenotype and molecular marker. Z1377 carried 18 substitution segments with average substitution length of 2.95 Mb. Compared with Nipponbare, Z1377 had significantly increased plant height, length of the 1st, 2nd, 3rd, and 4th internode, panicle length, number of primary and secondary branches and grain length, and decreased grain width, number of panicles per plant and seed setting ratio. However, the seed setting ratio was still 86.75%. Furthermore, F2 population from crosses between Nipponbare and Z1377 was used to map QTLs for plant height and other important agronomic traits. A total of 16 QTLs were detected, of which eight had been reported with the cloned genes such as GW2, EUI1, ZFP185, and the other eight were still not reported, such as qPH3. The plant height of Z1377 was mainly controlled by a major QTL (qPH3) with the explained phenotypic variance of 28.59% and a minor QTL (qPH5). Moreover, the high and dwarf plants basically displayed a bimodal distribution in the F2 population, and fitted to 3:1 segregation ratio by Chi-square test, indicating that high plant is dominant to dwarf plants and mainly conferred by qPH3. These results lay a foundation for fine mapping and cloning qPH3, meanwhile, also provide good bases for developing excellent chromosome segment substitution lines with moderate height plant carrying 2-3 substitution segments to be used in breeding.