As the main contributor to greenhouse gas (GHG) in paddy soil, information on methane (CH4) emission characteristics under different tillage and cultivation practices are limited. A five-year field trial was conducted from 2019 in a single-cropping rice system in Taihu Lake region, east of China. The experiment had a completely randomized block design, and the treatments included rotary tillage plus rice dry direct seeding (RD), rotary tillage plus rice mechanical transplanting (RT), and plowing tillage plus rice mechanical transplanting (PT). We determined the rice yield, GHG emission, soil traits, and methanogens and methanotrophs in 2022 and 2023. The results revealed that PT and RT significantly increased rice yield compared to RD, whereas PT simultaneously increased CH4 emissions. The year-averaged cumulative CH4 emissions in PT were increased by 38.5% and 61.4% higher than RT and RD, respectively. Meanwhile, yield-scaled global warming potentials (GWPs) in RT and RD were lower than those in PT. Tillage and cultivation practices shifted mcrA and pmoA abundances, and PT significantly decreased pmoA abundance. The community structure and diversity of the methanogens and methanotrophs were not significantly affected. Structural equation model analyses illustrated that CH4 emissions were regulated by mcrA and pmoA directly, which in turn, regulated by soil carbon and nitrogen. Overall, rotary tillage plus mechanism transplanting was a feasible agronomic technology in a single-cropping rice system in Taihu Lake region, exhibiting higher and more stable rice productivity, accompanied with lower CH4 emissions and yield-scaled GWP.