The time series of PALSAR-2 and Sentinel-1 images reveal inflation at the volcanic flank and contraction at the crater for approximately 5 months before the 2017 eruption of Shinmoe-dake volcano, Japan. While the observation of inflation at the volcano’s flank is ubiquitous, few studies have reported crater contraction preceding an eruption. The flank inflation stopped after the 2017 eruption, while the contraction at the crater continued until the 2018 eruption. We found that a pipe-shaped deformation source above sea level best fits the observation preceding the 2017 eruption. Suppose the flux of ejected materials constrains the conduit radius during the previous 2011 eruption. In that case, the amount of deformation of the pipe-shaped deformation source, whether open or closed at its top, is too large to be realistic. Although constraining the conduit radius from the eruption flux overestimates the pressure change of the pipe-shaped deformation source, water-saturated fractures along the volcanic conduit could extend the effective conduit radius of the pressure source. We propose one potential scenario for the mechanism of the crater contraction preceding volcanic eruptions based on the combination of compaction due to cooling by ambient groundwater and material withdrawal within the conduit. The groundwater inflows from the ambient aquifer through cracks in the porous conduit wall, which are generated by conduit expansion during the magma ascent. Decoupling from the conduit wall due to a decrease in volume of the material promotes material instability and crater contraction. The interaction between the groundwater and the magma triggers the 2017 eruption of Shinmoe-dake volcano, as previous studies have reported.Graphical