In order to explore the dietary iron sources on Cyprinus carpio (12.54 ± 1.65 g) and Lactuca sativa in aquaponic system, three semi-purified diets with iron contents of around 120 mg/kg were prepared: S-120 (ferrous sulfate); C-120 (ferrous citrate); and G-120 (ferrous glycinate). The results of 2 months trail showed that: (1) The final weight and weight gain of juvenile mirror carp in the C-120 and G-120 group showed a significant increase compared to those in the S-120 group (P < 0.05), and the feed conversion ratio in G-120 group significantly lower than the S-120 group (P < 0.05). (2) The fish muscle and whole-body iron content in the S-120 group were significantly lower than that in the C-120 group and G-120 group (P < 0.05). (3) The ∑n-3PUFA (mainly C22:6n-3) content of fish muscle in G-120 group were significantly higher than S-120 and C120 group (P < 0.05). (4) The liver superoxide dismutase activities in the G-120 and C-120 groups were significantly higher than the S-120 group (P < 0.05). The blood hematocrit level in the C-120 group was significantly higher than that in the S-120 group (P < 0.05). (5) The height, number of leaves, yield and chlorophyll of lettuce in the S-120 group were significantly higher compared to the G-120 group (P < 0.05). (6) The nitrogen utilization of fish in G-120 and C-120 groups was significantly higher than that in S-120 group (P < 0.05), and the nitrogen utilization of vegetables in S-120 and C-120 groups was significantly higher than that in G-120 group (P < 0.05). The total nitrogen utilization rate of S-120 group was higher than that of G-120 and C-120 groups (P < 0.05). Therefore, we suggested to use ferrous citrate as the iron source in feed of mirror carp to enhance the yield of fish and vegetables in the aquaponic system.