Influence of urea application on growth parameters (shoot height, and weight, root volume, weight and porosity; number of tillers; grain yield) and their relationship with methane (CH4) flux was investigated in Oryza sativa (var. Pant Dhan-4) under flooded soil condition. The study design consisted of (a) fertilized vegetated, (b) control vegetated, (c) fertilized bare, and (d) control bare plots. Crop growth and CH4 flux measurements were conducted from 9 to 115 days of rice transplanting at regular intervals of 10 days. Results showed that there were significant differences due to days (dates of measurement) and fertilization in all growth parameters except shoot height. Day × fertilization interaction was significant for all growth parameters. CH4 fluxes ranged from 0.4 to 20.2, 0.1 to 11.9, 0.09 to 2.2 and 0.004 to 1.5 mg m−2 h−1 under treatments (a), (b), (c) and (d), respectively. Maximum CH4 flux was recorded at the flowering stage. All the growth parameters, including number of tillers, showed strong positive relationship with total methane flux. Root porosity was also strongly correlated with total CH4 emission. It was concluded that CH4 emission was substantially influenced by crop phenology and growth, and fertilization. The study emphasizes the substrate production and conduit effects of rice plants on CH4 flux.