To evaluate the effects of iron supplementation on the growth performance, body composition and health status of mirror carp (Cyprinus carpio var. specularis) (10.34 ± 1.56 g), production of lettuce (Lactuca sativa var. ramosa Hort), and nitrogen utilization efficiency in media bed aquaponic system, a 60-day experiment was conducted. During the experiment, 0 (C), 1, 2, 3 and 4 mg/L iron chelate (ferrous glycinate) was added to fish tank of each system every 20 days. The results indicated as following: (1) Regarding the growth performance of mirror carp, the 1 mg/L group showed the highest weight gain (WG) and the lowest feed conversion ratio (FCR) when compared to the C group and the 4 mg/L group (P < 0.05). (2) In terms of body composition of mirror carp, the 1 mg/L group exhibited a significant increase in crude fat and iron content in the muscle (P < 0.05), and the ∑n-3 LCPUFA (C20:5n-3, EPA; C22:6n-3, DHA) was significantly higher in this group compared to the other groups (P < 0.05). (3) Regarding the health status of mirror carp, the 1 mg/L group had the highest liver catalase (CAT) activity, and the level of superoxide dismutase (SOD) activity was significantly higher than in the C, 3 mg/L, and 4 mg/L groups (P < 0.05). Liver malondialdehyde (MDA) content of mirror carp was significantly lower in 1 mg/L group compare to other groups (P < 0.05). (4) Concerning lettuce growth, the yield increased with rising iron content, and the group with 2 mg/L exhibited the highest chlorophyll content (P < 0.05). (5) Nitrogen utilization results showed that the 2 mg/L chelated iron group had the highest nitrogen utilization rate of 33.95%, while the C group had the lowest nitrogen utilization rate of 28.61%. Additionally, iron supplementation did not have a negative impact on the water quality of the aquaponic system. In summary, under the conditions of this study, adding 1 mg/L of chelate iron every 20 days in the aquaponic system is beneficial to the growth, body composition and health status of the mirror carp, the lettuce in the 2 mg/L group had better growth and yield. It is recommended to add 1–2 mg/L glycine chelated iron in the media bed aquaponic system every 20 days to promote the growth of fish and vegetables and improve the nitrogen utilization efficiency of the system.