The purpleback flying squid (Ommastrephidae: Sthenoteuthis oualaniensis) is an important species at higher trophic levels of the regional marine ecosystem in the South China Sea (SCS), where it is considered to show the potential for fishery development. Accordingly, under increasing climatic and environmental changes, understanding the nature and importance of various factors that determine the spatial and temporal distribution and abundance of S. oualaniensis in the SCS is of great scientific and socio-economic interest. Using generalized additive model (GAM) methods, we analyzed the relationship between available environmental factors and catch per unit effort (CPUE) data of S. oualaniensis. The body size of S. oualaniensis in the SCS was relatively small (<19.4 cm), with a shorter lifespan than individuals in other seas. The biological characteristics indicate that S. oualaniensis in the SCS showed a positive allometric growth, and could be suitably described by the logistic growth equation. In our study, the sea areas with higher CPUE were mainly distributed at 10°–11° N, with a 27–28 °C sea surface temperature (SST) range, a sea surface height anomaly (SSHA) of −0.05–0.05 m, and chlorophyll-a concentration (Chl-a) higher than 0.18 μg/L. The SST was the most important factor in the GAM analysis and the best fitting GAM model explained 67.9% of the variance. Understanding the biological characteristics and habitat status of S. oualaniensis in the SCS will benefit the management of this resource.