Abstract: In order to investigate the appropriate condition for the synthesis biodiesel by cottonseed oil in local Xinjiang and feat analysis method for the product,The influential factors of synthesizing biodiesel were investigated by single factor experiments and orthogonal test.The optimized reaction parameters were catalyst concentration 1.1%,alcohol/oil molar ratio 5:1,temperature 40℃,and reaction time 60 min.Under the optimal condition,Yield of cottonseed oil methyl esters were not less than 98.6%.The reactant Triglycerides and cottonseed oil biodiesel were quality and qualitative analysis by TLC method combined with HPLC firstly.The experiment result showed that the analysis method we bring forward have many advantages as follows:the sample can be analysised quickly;fatty acid methyl esters in biodiesel can be separated and have good linearity between its concentration and peak area(r2 0.99).This method is simple,fast and has a good reproducibility.