The side reactions in seawater and the sedimentation of the photocatalyst in highly concentrated ionic solutions seriously affect the activity and stability of the photocatalyst to split seawater to produce hydrogen. In terms of these problems, we designed the super-hydrophilic mesoporous brookite/anatase TiO2 photocatalyst accordingly. The characterization results of crystal phase and band structure confirmed that the transition from brookite/rutile type I hetero-phase junction to brookite/anatase type II hetero-phase junction. Without any sacrificial agents, the photocatalytic H2 production rate from seawater splitting reached 6.59 mmol g−1 h−1, which was 2.5 times and 2.9 times higher than brookite/rutile TiO2 and anatase/rutile TiO2 (P25), respectively. Meanwhile, it was also 4.4 times, 11.8 times and 36.1 times higher than brookite, anatase and rutile nanoparticles. Furthermore, the contact angle test confirmed the superhydrophilicity of the photocatalyst, mitigating the side reactions induced by Cl− and ensuring the long-term stability (100 h) of the photocatalyst in seawater.