Plant height (PH), heading date (HD) and productive panicle number (PN) are important agronomic trait in rice. Appropriate plant height, heading date and panicle number are prerequisites for the desired high and stable yield level in rice breeding programs. A recombinant inbred line (RIL) population consisting of 304 individuals was derived from a cross between indica varieties Zhong156 and Gumei2, from which a linkage map consisting of 168 RFLP, SSLP, RAPD and RGA markers that distribute on all the 12 rice chromosomes was constructed, and covers 1447.9 cM of the rice genome. The parents and 304 F9 lines were grown in the paddy field in China National Rice Research Institute (CNRRI), Hangzhou, China in 2001. The experiments were carried out in two seasons followed a randomized complete block design. QTLMapper 1.01 was applied to detect QTLs and QTL x environment (QE) interaction for HD (heading data), PH (plant height) and PN (panicle number), and conditional mapping for PH and PN was performed as well. A total of 15 QTLs with significant additive effects were detected, among which 4 QTLs had significant QE interaction. Ten QTLs with additive x additive epistatic effects for PH, HD and PN were detected, among which none showed significant epistatisis x environment interaction. These QTLs explained 12.12%, 1.38% and 5.00% of the total phenotypic variance for PH, HD and PN, respectively, and contributions were generally lower due to the strong epistatic effects. In conditional QTL analysis, the numbers of QTLs showing significant additive and epistatic effects were 7 and 6 for PH, and 3 and 3 for PN, respectively. Among the QTLs having significant additive effects for PH, qPH7-2 showed both additive effects and QE interaction, qPH7-1 and qPH10 showed QE interaction only, and the remaining 4 QTLs showed additive effects only. Each of the 3 QTLs having significant additive effects for PN did not display significant QE interaction. No epistatic QE interactions was detected. In addition, conditional QTL analysis indicated that the expression of QTLs for PH and PN may vary depending on the QTLs for HD.