In recent years, many rotational and integrated rice production systems coupled with several greenhouse gas (GHG) emissions mitigation practices have been developed and adopted for demand of low carbon production. However, there have been only few studies about comparisons on the balance between high production and mitigation of GHG emissions in different rice production systems. We therefore aimed to evaluate economic output and carbon footprint of different rice production systems, based on several long-term experiments conducted by our lab. CH4 and N2O emission were measured by the same static chamber/gas chromatogram measurement procedure in different rice production systems, including rice-fallow, rice-rapeseed, rice-wheat, double rice, and integrated rice-crayfish production system. Then, we applied the DeNitrification DeComposition model to simulate CH4 and N2O emission over different years under the same condition for comparison. Carbon footprint was calculated following the process-based life cycle assessment (PLCA) methodology. The economic benefit of rice production systems was assessed by cost-benefit analysis. According to the analysis, the double-rice production system exhibited the highest intensity of carbon footprint (ICF = 4.14 kg CO2-eq yuan?1), rain-fed treatment in the rice-rapeseed system had the lowest (ICF = 0.68 kg CO2-eq yuan?1). The intensity of carbon footprint in different treatments in the integrated rice-crayfish production system was around 0.8 kg CO2-eq yuan?1. Overall, the results of this case study suggest: (1) the proposed practices in different rice production systems are no straw returning (rice-fallow), no-tillage without straw returning (rice-wheat), rain-fed farming (rice-rapeseed), no insect and no inoculation (double rice), and feeding with straw returning (rice-crayfish); (2) rotational and integrated systems can achieve high net output with low carbon emission; (3) reducing the amount of nitrogenous fertilizer application is the most important and effective GHG mitigation practice for rotational systems.