In order to understand quantitative traits loci (QTLs) for complex traits in rice, in this study, the relationships, between the QTL of plant height and the QTL of main stalk height and panicle length, between the QTLs main stem height and updown 1, updown 2, updown 3, updown 4 and lower internode length, between the QTLs of grain length to width ratio and the QTLs of grain length and grain width, and between the QTLs of grain number per panicle and the QTL of primary branch number and secondary branch number. The results showed that: (1) 4 of 6 SSSLs detected were QTLs of main stem height with the percentage of additive effect, 86.00%-99.55%. One of 6 was QTL for panicle lengt with the percentage of additive effect, 48.31%. And, one was the QTLs for both main stem height and panicle length, with the percentage of additive effects, 81.72% and 18.28% respectively. (2) Out of the 7 SSSLs that detected with QTLs for the main stem height, one is with the QTL for updown1 internode length, two with SSSLs QTL for updown 2 internode length, and two with the QTL for updown 3 internode length, Two SSSLs were detected with QTL for updown 1 internode length and updown 2 internode length with the percentage of additive effect of QTLs for internode length ranging from –128.62% to 172.07% in different SSSLs. (3) Out of the 7 SSSLs that detected QTLs for grain length-to-width ratio, 5 SSSLs were the QTLs for grain length. (4) In three SSSLs detected as QTLs for grain number per panicle, 2 were QTLs for the number of secondary branches. In summary, the QTLs for constituent traits can be detected in the condition that QTLs for compound traits can be detected in the substitution segments. And, most of the additive effects of QTLs for compound traits can be analyzed by the combined effects of QTLs for constituent traits, with different QTLs of the constituent trait detected in different substitution segments