Paddy fields serve as a critical methane (CH₄) source and carbon dioxide (CO₂) sink, playing an essential role in terrestrial carbon cycling and greenhouse gas budgets. The effects of atmospheric turbulence on the vertical dispersion of CO₂ and CH₄ were investigated in this study, using high-frequency observations over subtropical paddy fields. The pronounced diurnal variations in surface concentrations and turbulent fluxes of both gases suggest the dominant control of boundary-layer turbulent diffusion. Focusing on nocturnal stable conditions, mutual information was introduced to characterize relevant nonlinear processes. Turbulence over the paddy fields becomes intermittent when the nighttime wind speed falls below 1.5 m s^−1. This weak and intermittent turbulence generally leads to the accumulation of CO₂ and CH₄ near the surface, whereas short turbulent bursts promote rapid dispersion, showing strong non-stationarity. Under intermittent turbulence, interference from submeso motions renders similarity relationships inapplicable for describing the transport of momentum, heat, as well as passive scalars (CO₂ and CH₄). This limitation can be effectively mitigated by removing submeso components from original observations. The distinct spectral gap between submeso and turbulent scales indicates the breakdown of energy cascade. As submeso energy is confined to its original scale, the energy supply for small-scale turbulence is limited and turbulence becomes more stochastic. This study reveals the effects of intermittent turbulence on the vertical diffusion of CO₂ and CH₄ under nocturnal stable conditions, but also highlights the challenges in parameterizing such stable-boundary-layer processes. This provides new insights for understanding carbon cycling over terrestrial ecosystems.