In order to explore the diffusion behavior of chloride ions in cracked cement mortar with high fly ash (FA) content, this study fabricated cement mortar specimens with different FA contents and crack widths by artificially prefabricating cracks. The chloride ion content in cracks was measured after natural soaking for 30 days and 60 days. The results show that the cracks accelerate the diffusion of chloride ions in cement mortar. The increase in the diffusion coefficient caused by 0.05 mm and 0.1 mm cracks is similar, while that caused by a 0.2 mm crack is significantly higher. After 30 days of soaking, the chloride ion content of the FA50 group decreases significantly with increasing depth beyond 10 mm. After 60 days of soaking, the chloride ion content of all specimens decreases significantly with increasing depth. When the fly ash content is not more than 40%, the chloride ion resistance of the mortar improves with increasing FA content. However, at 50% FA content, the chloride ion resistance sharply decreases. The relationship between crack width and the chloride ion diffusion coefficient follows a linear function, while the relationship between fly ash content and chloride ion diffusion coefficient can be described by a cubic function. A diffusion coefficient model considering both fly ash content and crack width has been established, and the validity of the model is verified by comparison between experimental values and fitted values.