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Leaf‐level photosynthetic capacity exhibits vertical variations along the canopy profile. The dynamics of photosystem energy partitioning involved in dissipating absorbed light energy, namely photochemical yield (ΦP), fluorescence yield (ΦF), and the efficiency of non‐photochemical quenching yield (ΦN) in dissipating excess light energy as heat, along the vertical canopy profile remain unclear. Here, vertical variations in photosystem energy partitioning and photosynthetic nitrogen allocation were measured at different canopy positions of rice using active fluorescence detection and photosynthetic gas exchange measurement in subtropical southern China. We observed the decline in leaf nitrogen per leaf mass (Nmass) from the top to the bottom of the canopy. ΦP significantly decreased from vegetative growth stage to ripening stage, while ΦN showed an opposite trend. The top and bottom leaves had consistent relationships between photosynthetic nitrogen allocation and photosystem energy partitioning. Our findings reveal the vertical variations in physiological traits of subtropical rice. Plain Language Summary: Photosystem energy partitioning refers to dissipating pathways of solar energy absorbed by plants, including photochemistry, nonphotochemical quenching, fluorescence and nonradiative decay. The relationship between these pathways is regulated not only by irradiance on short timescales, but also by vertical changes in the photosynthetic nitrogen distribution across these layers on long timescales. Our results explain the vertical variation in photosynthetic nitrogen allocation and energy partitioning. Leaves optimized photosynthetic nitrogen allocation to maximize energy capture in response to changes in environments, adapting across the vertical stratification within the canopy profile. The findings deepen our understanding of photosynthetic dynamics and light energy dissipation within the canopy. Key Points: ΦP significantly decreased from vegetative growth stage to ripening stage, while ΦN showed an opposite trendThe decline Nmass is attributed to self‐regulation in response to vertical fluctuations in the light environmentThe top and bottom leaves had consistent relationships between photosynthetic nitrogen allocation and photosystem energy partitioning [ABSTRACT FROM AUTHOR]