Since November 30, 2020, an intense seismic swarm and transient deformation have been continuously observed in the Noto Peninsula, central Japan, which is a non-volcanic/geothermal area far from major plate boundaries. We modeled transient deformation based on a combined analysis of multiple Global Navigation Satellite System (GNSS) observation networks, including one operated by a private sector company (SoftBank Corp.), relocated earthquake hypocenters, and tectonic settings. Our analysis showed a total displacement pattern over 2 years shows horizontal inflation and uplift of up to ~ 70 mm around the source of the earthquake swarm. In the first 3 months, the opening of the shallow-dipping tensile crack had an estimated volumetric increase of ~ 1.4 × 107m3at a depth of ~ 16 km. Over the next 15 months, the observed deformation was well reproduced by shear-tensile sources, which represent an aseismic reverse-type slip and the opening of a southeast-dipping fault zone at a depth of 14–16 km. We suggest that the upwelling fluid spread at a depth of ~ 16 km through an existing shallow-dipping permeable fault zone and then diffused into the fault zone, triggering a long-lasting sub-meter aseismic slip below the seismogenic depth. The aseismic slip further triggered intense earthquake swarms at the updip.