The complexity of marine gas hydrate systems at the Peruvian convergent margin has been linked to the post-Miocene history of vertical tectonics and subduction erosion that affected the forearc. Here, multichannel seismic data and published findings reveal that such a complexity has been further extended by the occurrence of the pre-Miocene deep Morsa Norte Graben (MNG) off Trujillo (8◦S–9◦S) in the Central Peru margin. At 650–750 m water depth in the upper slope, directly above the MNG depocenter (which has a 4–6 km overburden thickness), continuous bottom-simulating reflections (BSRs) and concentrated sub-BSR high-amplitude reflections are confined beneath a layered basin with low-to-moderate near-seafloor heat flow (7–33 mW.m −2 ). A deeper BSR modeled with a thermogenic gas composition is associated with the enhanced reflections. At 900 m water depth, sub-BSR reflections become less frequent in an area with a layered sediment cover defined by a moderate near-seafloor heat flow (15–33 mW.m −2 ). At 1200 m water depth, where the MNG is relatively thick (3–4 km overburden thickness), faults connect patchy BSRs with a moderate-to-high near-seafloor heat flow (52–110 mW.m −2 ). There, sub-BSR enhanced reflections are scarce. Immediately above the top of the gas hydrate stability zone (GHSZ), near-seafloor heat flow reaches 81 mW.m −2 . Modeling suggests a water depth dependent transport of heat toward the seafloor with respect to the top of the GHSZ, implying that the closer the seafloor to the top of the GHSZ, the lower the advection of heat and vice versa. Recent, seafloor-related depositional and structural features amplify such relations in agreement with near-seafloor heat flow variability. On the other hand, toward the area outside the extent of the MNG (<3 km overburden thickness), continuous BSRs are not linked either to a deeper BSR or sub-BSR enhanced reflections. The continuity of one of these BSRs is deflected upwards beneath a slump, suggesting an incomplete thermal re-equilibration of the GHSZ. Therefore, we conclude that the BSR responds to (1) the confinement and thickening of the free gas zone (FGZ) above the MNG depocenter due to the sealing effect of recent sedimentation close to the top of the GHSZ, (2) the seepage of gas-rich fluids from a thinned FGZ above the relatively thick MNG due to the allowing effect of faults cutting the GHSZ far from the top of the GHSZ, (3) the undisturbed state of the FGZ outside the extent of the MNG, and (4) the disequilibrium state of the base of the GHSZ due to the unloading of sediments in an unstable slope prone to failure.