Porphyrin-based photocatalytic materials have received great attention, and the effect of the substituents, central ions, and aggregated structure on the catalysis performance has been studied up to now. Herein, we report the effect of porphyrin isomerism on their aggregated structures as well as the photocatalytic activity. Two trans- and cis-porphyrin-based alternating copolymers with the same compositions (P1 and P2) are successfully synthesized. It is found that P1 self-assembles into propeller-like nanoparticles and P2 into multilayer hollow nanospheres. Furthermore, the hydrogen production rate of P1 (5533 μmol g-1 h-1) is 30 times higher than that of P2 (173 μmol g-1 h-1). Mechanism studies reveal that the high photocatalytic properties of P1 originate from the more ordered arrangement of porphyrins than P2, which facilitates the mobility and separation of photoinduced carriers. We believe the covalent and noncovalent polymer self-assembly process as well as the isomerism effect as disclosed here will shed new light on the design of high performance photocatalysts.