Abstract: Purpleback flying squid (Sthenoteuthis oualaniensis) is a typical epipelagic economic cephalopod in the South China Sea. It plays a crucial role in the material cycle of marine food webs. We collected 929 specimens from 22 stations in the southern South China Sea during 2016–2017, and measured 19 morphological traits. By performing analysis of variance (ANOVA), principal component analysis (PCA), and regression analysis, we investigated the sexual differences and spatial variation in morphological traits, and their correlations with environmental factors. The results show that mantle length, arm lengths, fin dimensions, body mass, stomach mass, and gonadal mass were significantly different between male and female individuals (p<0.01). Maturity had a great effect on the body mass, gonadal mass, head mass, and total stomach mass and other related traits. Female gonadal mass and male stomach mass showed the most pronounced spatial heterogeneity. Salinity had significant negative correlation with gladius morphological parameters, while current velocity was positively correlated with arm lengths (p<0.05), suggesting that salinity and current velocity played important roles in determining the functional traits. This study provides fundamental information for cephalopod resource assessment and management in the South China Sea.