Anaerobic batch experiments were conducted to study the regulatory role of endogenous iron in greenhouse gas emissions under intensive nitrogen fertilization in subtropical soils of China. Fe, Fe, and NO-N dynamics and NO, CH, and CO emissions, as well as the relationships between N fertilizer, endogenous iron, and greenhouse gas emissions were investigated. The emissions of NO increased to different extents from all the test soils by N1 (260 mg N kg) application compared with N0. After 24 days of anaerobic incubation, the cumulative emissions of NO from red soils in De'an (DR) were significantly higher than that from paddy soils in De'an (DP) and Qujialing (QP) under N1. However, N application enhanced CH and CO emissions from the red soils slightly but inhibited the emissions from paddy soils. The maximal CH and CO emission fluxes occurred in DP soil without N input. Pearson's correlation analysis showed that there were significant correlations (P< 0.01) between Fe and Fe, NO-N, (NO + N)-N concentrations in DP soil, implying that Fe oxidation was coupled with nitrate reduction accompanied by (NO + N)-N emissions and the endogenous iron played a regulatory role in greenhouse gas emissions mainly through the involvement in denitrification. The proportion of the electrons donated by Fe used for NO production in denitrification in DP soil was approximately 37.53%. Moreover, positive correlations between Fe and CH, CO were found in both DR and QP soils, suggesting that endogenous iron might regulate the anaerobic decomposition of organic carbon to CH and CO in the two soils. Soil pH was also an important factor controlling greenhouse gas emissions by affecting endogenous iron availability and C and N transformation processes.