Carbon Nitride is considered as a promising photocatalyst material because of its unique properties such as environment-friendly, suitable band gap and high stability. However, the photocatalytic activity of pristine g-C3N4 was greatly hindered by the recombination of photo-generated electron-hole pairs. In this work, we provide an alternative method to address this problem by the construction of g-C3N4 isotype heterojunction (CNH-T/CNH-U) structure, which was successfully synthesized by a facile protonation assisted hydrothermal method. Under the irradiation of visible light (lambda > 420nm), the CNH-T/CNH-U isotype heterojunction photocatalyst displays much higher photodegradation activity of organic dyes degradation and H-2-production activity than the pure CNH-T or CNH-U sample. This remarkably improved photocatalytic performance is attributed to the successful construction of CNH-T/CNH-U isotype heterojunction associated by protonation, which results in larger surface area and the more efficient separation of photo-generated electron-hole pairs, further investigated by electron paramagnetic resonance, photoluminescence, photocurrent measurement, and a series of active species trapping experiments.