Ensuring efficient iron absorption by crops is crucial in terms of high crop yields and food security. Bio-based materials effectively transport nutrients with minimal environmental impacts. Here, highly efficient lightweight iron fertilizers, CSG@Fe was prepared using chitosan hydrogels (CSG) as the adsorption carrier. Iron release from the various CSG@Fe preparations was slow under neutral conditions but rapid under acidic conditions. The effects of various cross-linking agents were investigated; 1.0 wt.% genipin chitosan hydrogels iron fertilizer (GE-CSG@Fe) evidenced an excellent iron adsorption rate and a higher iron loading (326.15 mg/g) than the other two iron fertilizers. Iron release from CSG@Fe materials followed the Korsmeyer-Peppas model. Notably, wheat seed germination and tomato pot experiments revealed that GE-CSG@Fe significantly enhanced germination and growth. GE-CSG@Fe appropriately reduced the soil pH, protected ferrous ions from soil oxidation and rapid fixation, activated the soil microenvironment, and improved nutrient absorption by the roots of crops growing. This work provides a simple and effective strategy for overcoming constraints in the development and application of iron fertilizers and provides insights into the development of green and efficient iron fertilizers with intelligent response properties.