Understanding the effective light energy absorption cross-section of chlorophyll molecules is crucial for a deeper insight into the complexities of the plant photosynthetic process. This study investigates how the effective energy absorption cross-section of chlorophyll responds to varying light intensities, aiming to shed light on the underlying reasons for discrepancies in photosynthetic electron transfer rates among plants exposed to different light conditions. We used a portable photosynthesis fluorescence measurement system to capture the response curve of the electron transfer rate to light intensity (J/I curve) for soybean (Glycine max) leaves under both shaded and full sunlight conditions, with each condition tested across CO₂ concentrations of 300, 400, 500 μmol/mol and 600 μmol/mol. Concurrently, we measured the chlorophyll content of the soybean leaves to provide a comprehensive dataset. Using a photosynthetic mechanistic model, we calculated key parameters: the intrinsic light absorption cross-section (σ_ik), the effective light absorption cross-section (σ'_ik), and the minimum average lifetime (τ_min) of the excited state of the pigment molecules. The mechanistic model showed an excellent fit to the J/I curves of soybean leaves under the tested CO₂ concentrations and light conditions, with a determination coefficient exceeding 0.99. The fitted results revealed significant differences in the maximum electron transport rate values (J_max) between shaded and full sunlight conditions across all CO₂ concentrations. Specifically, J_max values ranged from 126.03 to 164.34 μmol m^-2 s^-1 under shade and 273.33 to 326.92 μmol m^-2 s^-1 under full sunlight. Similarly, τ_min exhibited distinct ranges: 16.15 to 22.93 ms under shaded conditions and a notably lower range of 3.65 to 4.64 ms under full sunlight. In comparing the two light conditions, the photosynthetic pigment molecules in soybean leaves demonstrated a significantly lower light energy absorption capacity under shade, yet they possessed a higher number of chlorophyll molecules in the lowest excited state. Notably, the values of σ_ik and τ_min were not significantly affected by varying CO₂ concentrations under the same light conditions. In contrast, the σ'_ik value decreased as CO₂ concentrations increased. By integrating the calculation formula of the electron transfer rate with relevant photosynthetic parameters at 400 μmol/mol CO₂ concentration, our study quantitatively explains why soybean leaves exhibit a higher J_max under full sunlight. This explanation is based on the light energy absorption characteristics of chlorophyll molecules, providing a novel perspective on the role of pigment molecules in photosynthesis. This research not only advances our understanding of photosynthetic efficiency under varying environmental conditions but also introduces a new methodological approach for quantitatively analyzing the effective energy absorption cross-section of chlorophyll molecules. These advancements are vital for optimizing agricultural practices and managing plant growth in response to changing light conditions and atmospheric CO₂ levels.