Crystalline carbon nitride (CCN) has emerged as a highly promising semiconductor photocatalyst with unique properties, such as enhanced charge migration rate, reduced carrier recombination probability, narrow band gap and improved light-harvesting efficiency, which are suitable for a wide range of applications in solar-to-chemical conversion, energy storage, therapeutic and environmental pollution degradation. In the past few years, there has been an increasing number of reviews on CCN materials. However, most of these reviews mainly focus on synthesis methods, modification and applications, with less emphasis on the relationship between structures and properties, as well as on in-depth exploration of the crystalline structure. The electronic instability of CCN presents challenges for conventional characterization techniques to directly and thoroughly investigate the relationship between its intrinsic atom structure and photocatalytic performance. This mini-review not only highlights the progress in CCN-based photocatalysts, with a focus on molten-salt synthesis (including solid-salt-induced crystallization), but also emphasizes the atomic structure characterization by specifically introducing the differential phase contrast (DPC) scanning transmission electron microscopy (STEM) technique, which is essential for enhancing our understanding of the crystal structure and photocatalytic mechanisms of CCNs. Additionally, the review outlines the photocatalytic performance and puts forward potential challenges on CCN studies. This review will provide a clearer understanding of the relationship in developing precise customization strategies for CCN materials and ultimately explain the regularity and specificity of the enhanced performance in targeted photocatalytic systems.