The yield and earliness-related traits of the sea-island cotton were identified to provide DNA molecular markers for using in cotton improvement in the future. A genetic linkage map of sea-island cotton was constructed by using 190 F2: 3 family lines derived from two sea-island cotton cultivers (Xinhai 3 and Jiza 82) with 107 polymorphic primer pairs obtained by screening among 5000 SSR primer pairs. The linkage map covered 20.12% of the whole cotton genome which including 22 linkage groups, 74 markers, a whole length of 893 cM with an average interval of 12.06 cM between two markers by Joinmap3.0 software. Based on composite interval mapping. 21 QTLs related with yield and earliness traits of the sea-island cotton were detected. 12 QTLs associated with earliness traits were respectively located on linkage groups LG1 LG3 LG5 LG6、LG11、LG17, LG22 , and 9 QTLs associated with yield traits were respectively located on linkage groups LG4、LG5、LG6、LG16、LG22. This research could provide valuable information for the molecular design breeding of yield and earliness in sea-island cotton.