Covalent triazine frameworks (CTFs) represent promising polymeric photocatalysts for photocatalytic hydrogen production with visible light. However, the separation and transfer of charges in CTFs are isotropic because of the uniform distribution of donor–acceptor motifs in the skeleton. Herein, to achieve the anisotropic charge carrier separation and migration, thiophene (Th) or benzothiadiazole (BT) unit is selected as the dopant to modify the molecular structure of CTF‐based photocatalysts. Both theoretical and experimental studies reveal that the incorporation of Th or BT units induces the anisotropic charge carrier separation and migration at the interface of CTFs. The optimized polymer manifests a much enhanced photocatalytic activity for photocatalytic hydrogen production with visible light, and thus this study provides a useful tool to design conjugated polymer photocatalysts at the molecular level for solar energy conversion. Anisotropic charge carrier separation and migration are obtained by the rational design of the molecular structure of covalent triazine frameworks (CTFs). Both theoretical and experimental results prove the enhanced optical absorption, fast charge carrier transfer, and promoted photocatalytic hydrogen production performance of the modified CTFs in comparison with the pristine sample.