Helium (He) in hydrological systems is used to constrain the deep structure and improve interpretations of geophysical techniques beneath the Cathaysia Block (CB), of which the Cenozoic tectonic and geodynamic processes are controversial. The air-corrected 3He/4He ratio of both geothermal and non-geothermal waters in the CB range from 0.10 to 6.41Ra (Ra is the atmospheric 3He/4He ratio), displaying an increasing trend from inland to coastal area, aligning with thinning crust and younger magmatic activities. Mantle-derived He fluxes in the CB vary from 0.11 to 33.41 × 1010 atoms m−2s−1, surpassing those in stable continental areas by up to three orders of magnitude. Due to the absence of active volcanic surface manifestations and identifiable crustal magma chambers, the mantle-derived volatiles are possibly transported from the mantle through the faults with advective flow rates ranging from 1.26 to 154 mm y−1. Two distinct modes of mantle He releases lead to differences in mantle He fluxes between the interior and coastal CB. Seismic activity enhances permeability in the interior CB, leading to the leakage of mantle He. In the coastal CB, high mantle He fluxes with characteristics of volcanic degassing imply degassing from the partial mantle melting. The presence of high 3He/4He ratios (up to 6.41 Ra) and regional thermal anomaly provide evidence for an ongoing process of crustal underplating by mantle melting. Combined with the underplate layer revealed by geophysical results, this implies the continuous compensation mechanism involving mantle influx to counter extension-induced crustal thinning since the Mesozoic–Cenozoic in the coastal CB.