Submarine volcano monitoring is vital for assessing volcanic hazards but challenging in remote and inaccessible environments. In the vicinity of Kita-Ioto Island, south of Japan, unusual M~5 non-double-couple volcanic earthquakes exhibited quasi-regular repetition near a submarine caldera. Following the 2008 earthquake, a distant ocean bottom pressure sensor recorded a distinct tsunami signal. In this study, we aim to find a source model of the tsunami-generating earthquake and quantify the pre-seismic magma overpressure within the caldera’s magma reservoir. Based on the earthquake’s atypical focal mechanism and efficient tsunami generation, we hypothesize that submarine trapdoor faulting occurred due to highly pressurized magma. To investigate this hypothesis, we establish a mechanical earthquake model that links pre-seismic magma overpressure to the size of the resulting trapdoor faulting, by considering stress interaction between a ring-fault system and a reservoir of the caldera. The model reproduces the observed tsunami waveform data. Our estimates indicate trapdoor faulting with large fault slip occurred in the critically stressed submarine caldera accommodating pre-seismic magma overpressure of ~10 MPa. The model infers that the earthquake partially reduced magma overpressure by 10–20%, indicating that the magmatic system maintained high stress levels even after the earthquake. Due to limited data, uncertainties persist, and alternative source geometries of trapdoor faulting could lead to estimate variations. These results suggest that magmatic systems beneath calderas are influenced much by intra-caldera fault systems. Monitoring and investigation of volcanic tsunamis and earthquakes help to obtain quantitative insights into submarine volcanism hidden under the ocean.