Grass carp (Ctenopharyngodon idella) is an important economic freshwater fish in China. Under intensive aquaculture conditions, the farmed grass carps often display excess fat accumulation, such as fatty liver, rotund shape and increased body lipid content. To evaluate the possibility of genetic improvement, this study estimated the phenotypic variability and correlation of lipid traits in C. idella. A total of 15 quantitative traits of 17 month-old C. idella among 296 individuals were analyzed by mathematical statistical methods. The results showed that intraperitioneal fat index IPF, hepatopancreas lipid content HLC and muscle lipid content MLC had high variation in C. idella, and the phenotypic variation coefficients ranged from 21.30% to 47.04%. Correlation analysis showed that there was a significant positive correlation among the three lipid traits, suggesting that the process of lipid deposition has a certain synchronization in different tissues of C. idella. Furthermore, factor and cluster analysis revealed that the observed 15 quantitative traits were roughly divided into 4 categories:body shape factor, body size factor, organ index factor, and body lipid content factor. IPF belonged to organ index factor, while HLC and MLC formed body fat content factor together. In addition, multivariate statistical analysis showed that the explanation degree of morphological traits on the variation of the three lipid traits ranged from 7.45% to 24.83%. By contrast, sagittal shape SS can, to some extent, predict body lipid traits. In summary, the lipid traits of C. idella have great potential for genetic improvement, and IPF would be an attractive character as breeding target. This study provided important reference for genetic improvement of lipid traits in C. idella.