The Gulf of California and adjacent Pacific have passed through a prolonged warming period that affects the Humboldt squid D. gigas life cycle, which was the third largest fishery in Mexico until its total collapse after 2010. The aims of the present study were (i) to characterize the nursery habitat of paralarvae of the complex Sthenoteuthis oualaniensis–Dosidicus gigas (SD complex) on the basis of 1112 paralarvae collected from zooplankton trawls carried out during ten oceanographic cruises off northwestern Mexico between 2010 and 2017; and (ii) to model the seasonal and interannual variability of the nursery habitat, applying a generalized additive model (GAM) using a regional long-term (1922–2017) hydrographic database. The GAM showed significant relationships of paralarvae abundance with the seasonal average of thermocline depth, absolute salinity, and conservative temperature. The potential nursery habitat of the SD complex paralarvae showed its maximum expected abundance in the entrance of the Gulf of California during spring, when the thermocline depth was shallowest (<30 m). During summer the nursery habitat moved northward along the Pacific west coast of the peninsula. Autumn and winter were less suitable seasons for paralarvae nursery because the thermocline was deep throughout the area of study. Potential nursery habitat did not change interannually in location during La Niña conditions, but did increase the expected abundance in its southern extension. El Niño events contracted the nursery habitat near Cabo San Lucas, and caused the habitat to move northwards over both coasts of the Baja California peninsula. Despite seasonal and interannual climatic variability, two regions remained suitable habitats almost throughout the year. One was associated with coastal upwelling regions (Cabo Corrientes) and the second comprised the oceanic region of high mesoscale kinetic energy located south of Cabo San Lucas. We conclude that the potential nursery habitat of the SD complex is more coastal than oceanic, and is associated with a shallow thermocline in the tropical-subtropical convergence off Mexico. The recent anomalous warming period in this region could drive the changes in the morphology of D. gigas in the Gulf of California, given the effects of environmental variability over early stages of development throughout the adult ontogenesis.