It has long been known that there is a conical intersection (CI) between the ground and first excited electronic state in the H3 system. Its associated geometric phase (GP) effect has been theoretically predicted to exist below the CI since a long time. However, the experimental evidence has not been established yet and its dynamical origin is waiting to be elucidated. Here we report a combined crossed molecular beam and quantum reactive scattering dynamics study of the H+HD → H2+D reaction at 2.28 eV, which is well below the CI. The GP effect is clearly identified by the observation of distinct oscillations in the differential cross section around the forward direction. Quantum dynamics theory reveals that the GP effect arises from the phase alteration of a small part of the wave function, which corresponds to an unusual roaming-like abstraction pathway, as revealed by quasi-classical trajectory calculations.