Charge transfer, which is closely related to the molecular structure and packing order of polymer semiconductors, plays a critical role in determining their photocatalytic performance. Metal poly(heptazine imides) (M-PHI), with visible-light absorption capacity, represent a promising class of photocatalysts for energy and environmental applications. A precise understanding of the configuration of their building units and the resulting structure-function relationship is essential to the rational design of advanced polymer materials. In this study, advanced characterization techniques, including the iDPC-STEM, combined with density functional theory (DFT) calculations, are employed to reveal the local molecular structures of M-PHI (M = Na+, K+, Rb+, Cs+) crystals after ion insertion and to establish the intrinsic relationship between charge-carrier transfer and packing modes. Na+ maintains the hexagonal symmetry of PHI through uniform coordination, thereby preserving long-range π-conjugation and enabling the highest charge-carrier mobility, whereas larger cations induce structural distortions in other M-PHI crystals by disrupting the heptazine packing symmetry. The higher symmetry and shorter intermolecular distances in Na-PHI endow it with rapid charge-transfer rates and excellent photocatalytic performance compared to other M-PHI samples. This study provides fundamental insights into the connection between atomic structure and charge-transport properties in PHI materials and establishes a theoretical foundation for the rational design of conjugated polymer semiconductors with optimized charge mobility for photocatalytic applications.