Quantifying the carbon footprint of crop production can help provide a theoretical basis to mitigate greenhouse gas emissions in agro-ecosystem. In this study, the life cycle assessment was used to assess the carbon footprint of two cropping systems (early rice-late rice continuous cropping system and spring maize-late rice rotation systems) and quantitatively analyze the relative contribution of various carbon sources in grain production in paddy field of Southern China. The results showed that the spring maize-late rice rotation reduced the carbon emissions per unit area by 6724 kg CO₂-eq/hm² and the carbon footprint per unit yield by 0.56 kg CO₂-eq/kg compared with the continuous cropping of early rice-late rice. The carbon emissions from the production of spring maize were less 6228 kg CO₂-eq/hm² than in early rice. The carbon emissions of late rice in spring maize-late rice rotation system were decreased by 497 kg CO₂-eq/hm², when compared with that in early rice-late rice system. The main components of carbon footprint in the early rice-late rice planting system were derived from the carbon emission of methane (CH₄) from paddy field (9776kg CO₂-eq/hm², 54.8%), nitrogen fertilizer production and application (2871 kg CO₂-eq/hm², 16.1%), and electricity consumption (2849 kg CO₂-eq/hm², 16.0%). While the main part of carbon footprint came from the carbon emission of CH₄ (4442 kg CO₂-eq/hm², 40.0%), nitrogen fertilizer production and application (2871 kg CO₂-eq/hm², 25.8%), and electricity consumption (1508 kg CO₂-eq/hm², 13.6%) in the spring maize-late rice rotation system. The composition of carbon footprint of late rice in this system were similar to that in the spring maize-late rice system. However, the main part of carbon footprints of spring maize were mainly derived from the carbon emission of nitrogen fertilizer production and application (1435 CO₂-eq/hm², 50.1%), nitrous oxide (579 kg CO₂-eq/hm², 20.2%), and CH₄ (378 CO₂-eq/hm², 13.2%). Meanwhile, compared with the yield of late rice (6333 kg/hm²) in early rice-late rice cropping system, the yield of late rice (7271 kg/hm²) was increased in the spring maize-late rice rotation system. Accordingly, introducing spring maize-late rice rotation system is conducive to improving rice paddy productivity and mitigating carbon emission and carbon footprint in continuous rice systems.