Organic cultivation plays an important role in improving the quality of chrysanthemum. Chitosan organic water-soluble fertilizer, as a new organic fertilizer, has been widely used in fruits and vegetables. In this study, 5 treatments were designed for a pot experiment, which included: no fertilizer (CK), chitosan organic water-soluble fertilizer diluents of 1000×(T1), 500×(T2), 300×(T3) and 100×(T4). The effects of these treatments on the biomass, growth and development index, root morphological characteristics, photosynthesis, carbon and nitrogen contents and carbon and nitrogen ratio of chrysanthemum were analyzed. The results showed that compared with CK treatment, the fresh weight of root, fresh weight of aboveground, leaf number, stem diameter and plant height of T3 treatment significantly increased by 64%, 110%, 27%, 17% and 32%, respectively, which indicated that the optimum amount of organic chrysanthemum seedling was 300 times diluted by organic water-soluble fertilizer of chitosan. In addition, compared with CK, the total root length, root surface area and root volume of T3 treatment increased by 46%, 62% and 69%, respectively, and the photosynthesis rate increased by 64%, and the carbon and nitrogen ratio in the seedling stage of chrysanthemum was adjusted, and the values of carbon and nitrogen ratio in the root system and the aboveground part were 19 and 17, respectively. In conclusion, the promotion of chitosan organic water-soluble fertilizer to the growth of organic chrysanthemum in seedling stage could be attributed to improving root morphological characteristics, enhancing photosynthesis and regulating plant carbon and nitrogen ratio.