This study investigated the factors influencing the formation of fishing grounds for the neon flying squid (Ommastrephes bartramii), whose importance has increased due to the recent decline in Japanese common squid (Todarodes pacificus) resources since around 2015–2016. Using catch data from squid jigging vessels operating from May to July between 2019 and 2022, together with oceanographic data from the Hybrid Coordinate Ocean Model (HYCOM), we analyzed the three-dimensional (3D) temperature structure of O. bartramii habitat. Kernel density estimation was applied to characterize temperature distributions and to quantify the presence or absence of thermal frontal structures at specific temperatures. A generalized linear mixed model was then used to examine the relationship between these thermal fronts and catch per unit effort. The results indicated that the presence of frontal structures at 8°C-10°C in May, 8°C in June, and 6°C-10°C in July was associated with increased catches. These findings suggest that not only surface temperatures, but also intermediate-water thermal gradients play an important role in the formation of O. bartramii fishing grounds and that incorporating 3D environmental information could improve the accuracy of fishing-ground prediction models.