Agricultural fertilization may change processes of elemental biogeochemical cycles and alter the ecological function. Ecoenzymatic stoichiometric feature plays a critical role in global soil carbon (C) metabolism, driving element cycles, and mediating atmospheric composition in response to agricultural nutrient management. Despite the importance on crop growth, the role of phosphorous (P) in compliance with eco-stoichiometry on soil C and nitrogen (N) sequestration in the paddy field remains poorly understood in the context of climate change. Here, we collected soil samples from a field experiment after 6 years of chemical P application at a gradient of 0 (P-0), 30 (P-30), 60 (P-60), and 90 (P-90) kg ha-1 in order to evaluate the role of P on stoichiometric properties in terms of soil chemical, microbial biomass, and eco-enzyme activities as well as greenhouse gas (GHG: CO2, N2O and CH4) emissions. Continuous P input increased soil total organic C and N by 1.3-9.2% and 3%-13%, respectively. P input induced C and N limitations as indicated by the decreased ratio of C:P and N:P in the soil and microbial biomass. A synergistic mechanism among the ecoenzymatic stoichiometry, which regulated the ecological function of microbial C and N acquisition and were stoichiometrically related to P input, stimulated soil C and N sequestration in the paddy field. The lower emissions of N2O and CH4 under the higher P application (P-60 and P-90) in July and the insignificant difference in N2O emission in August compared to P-30; however, continuous P input enhanced CO2 fluxes for both samplings. There is a technical conflict for simultaneously regulating three types of GHGs in terms of the eco-stoichiometry mechanism under P fertilization. Thus, it is recommended that the P input in paddy fields not exceed 60 kg ha-1 may maximize soil C sequestration, minimize P export, and guarantee grain yields.