Accurate partitioning of net ecosystem exchange (NEE) of CO2 to gross primary production (GPP) and ecosystem respiration (Reco) is crucial for understanding carbon cycle dynamics under changing climate. However, it remains as a long-standing problem in global ecology due to lack of independent constraining information for the two offsetting component fluxes. Solar-Induced chlorophyll Fluorescence (SIF), a mechanistic proxy for photosynthesis, holds great promise to improve NEE partitioning by constraining GPP. We developed a parsimonious SIF-based approach for NEE partitioning and examined its performance using synthetic simulations and field measurements. This approach outperforms conventional approaches in reproducing simulated GPP and Reco, especially under high VPD. For field measurements, it results in lower daytime GPP and Reco than conventional approaches. This study made the first attempt to demonstrate SIF’s potential for improving NEE partitioning accuracy and sets the stage for future efforts to examine its robustness and scalability under real-world environmental conditions.