Abstract: Both modern molecular biology technique and new statistical methods greatly promoted the analysis of plant quantitative trait loci (QTL). Linkage mapping (LM)and association mapping (AM) are two important methods for QTL analysis. Both them have obvious complementarity in the accuracy and breadth of QTL mapping, the provided information, and the statistical analysis method. Linkagemapping can preliminary locate the target trait gene, while association mapping can quickly achieve the verification and fine mapping of target gene; moreover, it can also verify the candidate gene function according to a lot of information provided for a specific candidate gene. In this paper, the new advances were reviewed from the linkage mapping and association mapping of cotton quantitative traits. The research prospects of cotton QTL were analyzed by combining the two methods.·