In this study， five fiber quality indexes（ Fiber upper half mean length FUHML， Fiber strength FS， Micronaire value MV， Fiber elongation FE， Fiber uniformity FU） of 214 upland cotton materials were tested under seven environments， and Boxplot were drew by SPSS19.0， and the heritability， correlation and phenotypic effect values of the traits were calculated by using the phenotypic data analyzed by BLUP. 259 SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphism in 214 cotton materials， the polymorphism information of primers were calculated by PowerMarker 3.25， and molecular marker data and phenotypic traits were analyzed by the method of GLM（ General Linear Model）（ Q） in TASSEL software， phenotypic effect values were used to identify excellent allelic variants and typical materials carrying elite alleles. The result showed that the same one fiber quality trait had a relatively stable change trend in two to three years in three regions. There were positive correlations among FUHML， FS and FU（ P<0.01）， and FUHML/FS and MV/FE were negatively correlated. A total of 309 alleles and 774 genotypes were detected. The average polymorphic information content（ PIC） per marker was 0.2688， and the average genetic diversity index was 0.2239. Two hundred and fourteen upland cotton materials were divided into two subgroups by analysis of population genetic structure. A total of 134 loci associated with fiber quality traits were detected（ P<0.01）， among them， thirty loci could be detected stably in three or more environments. Three loci（ NAU6177， DPL0886， NAU3607） were found to be significantly associated with FUHML/FS， MV and FE respectively in seven environments（ P<0.01）， the maximum explanation rate up to 11.14%， 5.74% and 13.99% respectively. Thirty-one loci related to more than two fiber traits simultaneously， including the loci near NAU6177 related to aforementioned five fiber quality indexes（ P<0.01） . Compared with reported results， seventeen QTLs in this study has been reported to be related to fiber quality，in which 10 QTLs associated with the same traits. Based on the results， seventy-two alleles related with fiber quality were identified by phenotypic effect analysis respectively. Specifically， the allelic variation loci with the maximum increasing effect of FUHML， FS， MV and FE were NAU5387b（ +0.95 mm）， NAU5387b（ +1.25 cN/tex）， NAU943a（ +0.40）， and COT002a（ +0.62） respectively， and the allelic variation loci with the maximum decreasing effect of FUHML， FS， MV and FE were NAU6177e（ -1.21 mm）， NAU6177d（ -1.43 cN/tex）， CIR286b（ -0.78）， and NAU5387b（ -0.40） separately. Furthermore， five typical materials carrying elite alleles were selected， which were Ji 228（ FUHML）， Xinluzao 25（ FUHML， FS）， Ji N71（ FS）， Xinluzhong 36（ MV） and Xuzhou 142（ FE） . In conclusion， stable molecular markers associated with fiber quality were revealed by association analysis， and elite alleles and typical materials carrying elite alleles were identified， which could provide a reference for molecular assisted selection of upland cotton about fiber quality.