During free exploration, the emergence of patterned and sequential behavioral responses to an unknown environment reflects exploration traits and adaptation. However, the behavioral dynamics and neural substrates underlying the exploratory behavior remain poorly understood. We developed computational tools to quantify the exploratory behavior and performed in vivo electrophysiological recordings in a large arena in which mice made sequential excursions into unknown territory. Occupancy entropy was calculated to characterize the cumulative and moment-to-moment behavioral dynamics in explored and unexplored territories. Local field potential analysis revealed that the theta activity in the dorsal hippocampus (dHPC) was highly correlated with the occupancy entropy. Individual dHPC and prefrontal cortex (PFC) oscillatory activities could classify various aspects of free exploration. Initiation of exploration was accompanied by a coordinated decrease and increase in theta activity in PFC and dHPC, respectively. Our results indicate that dHPC and PFC work synergistically in shaping free exploration by modulating exploratory traits during emergence and visits to an unknown environment. © 2021 Science China Press