A field experiment was conducted to (i) examine the diurnal and seasonal soil carbon dioxide (CO2) fluxes pattern in rice paddy fields in central China and (ii) assess the role of floodwater in controlling the emissions of CO2 from soil and floodwater in intermittently draining rice paddy soil. The soil CO2 flux rates ranged from −0.45 to 8.62 µmol.m−2.s−1 during the rice-growing season. The net effluxes of CO2 from the paddy soil were lower when the paddy was flooded than when it was drained. The CO2 emissions for the drained conditions showed distinct diurnal variation with a maximum efflux observed in the afternoon. When the paddy was flooded, daytime soil CO2 fluxes reversed with a peak negative efflux just after midday. In draining/flooding alternating periods, a sudden pulse-like event of rapidly increasing CO2 efflux occured in response to re-flooding after draining. Correlation analysis showed a negative relation between soil CO2 flux and temperature under flooded conditions, but a positive relation was found under drained conditions. The results showed that draining and flooding cycles play a vital role in controlling CO2 emissions from paddy soils.