Greenhouse gas (GHG) emissions from rice paddies have gained widespread attention, and fertilization management can mitigate GHG emissions. Red paddy soils in southern China are characterized by phosphorus (P) deficiency, requiring fertilization management. In the present study, soils from a red paddy field were used in a pot experiment with 5 levels of P application (P1–P5: 0, 22.5, 45, 90, 113, 135 kg ha⁻¹, respectively) to investigate growth and yield of rice (Oryza sativa L.) and carbon dioxide (CO₂) and methane (CH₄) emissions from soils. P application increased photosynthetic rate, tiller number, plant biomass and yield. All P treatments decreased CH₄ emission at the tillering stage but increased it at the filling and maturing stages, causing decreases in cumulative CH₄ emission under P1, P2, and P4. Cumulative CO₂ emission did not significantly differ among P0–P3 but increased by P4 and P5. Cumulative CO₂ and CH₄ emissions were positively correlated with plant height, implying that changes in plant structure such as aerenchyma might be attributable to GHG emissions. Overall, P application of 89 kg ha⁻¹ was sufficient to reduce GHG emissions and enhance rice yield. These results provide a reference for adjusting P management in red paddy fields.