Molybdenum disulfide (MoS2) with the two-dimensional layered structure has been widely studied as an advanced catalyst for hydrogen evolution reaction (HER). Intercalating guest species into the van der Waals gaps of MoS2 has been demonstrated as an effective approach to tune the electronic structure and consequently improve the HER catalytic activity. In this work, by constructing nanostructured MoS2 particles with largely exposed edge sites on the three-dimensional substrate and subsequently conducting Li electrochemical intercalation and exfoliation processes, an ultrahigh HER performance with 200 mA/cm2 cathodic current density at only 200 mV overpotential is achieved. We propose that both the high surface area nanostructure and the 2H semiconducting to 1T metallic phase transition of MoS2 are responsible for the outstanding catalytic activity. Electrochemical stability test further confirms the long-term operation of the catalyst.