Solar-induced chlorophyll fluorescence (SIF) is a promising photosynthetic proxy and a valuable phenotyping tool. However, under drought and fluctuating light, the mechanistic linkages between SIF and photosynthesis require further investigation due to complex light energy partitioning. In this study, we measured leaf-level SIF, gas-exchange, and active fluorescence parameters in Ginkgo biloba under drought and fluctuating light. Our results demonstrate a drought-induced decoupling of both leaf-level SIF and PSII-emitted chlorophyll fluorescence (SIF_PSII, derived from active fluorescence parameters) from photosynthesis. This was driven by a slight SIF_PSII reduction alongside strong photosynthetic suppression. The limited SIF_PSII decrease resulted from a stable fluorescence yield (Φ_SIF), maintained by the regulatory interplay between non-photochemical quenching (NPQ) and the fraction of open PSII reaction centers (q_L), and the low responsiveness of Φ_SIF to changes in the maximum photochemical quantum yield (Φ_PSIImax). In contrast, photosynthetic suppression was largely due to decreased stomatal conductance (g_s). Φ_PSIImax and photorespiration are also central to balancing the light and carbon reactions, preventing energy overload. Interestingly, fluctuating light phases did not significantly alter this decoupling. However, when combining data from both high and low light, SIF_PSII and photosynthesis remained tightly coupled, likely due to their shared light dependency. These insights improve the physiological interpretation of SIF and underscore the importance of SIF-based multi-trait phenotyping models for accurate field monitoring.