The coupling of solar-induced chlorophyll fluorescence (SIF) and gross primary production (GPP) is the foundation of SIF-based GPP estimations; however, the relationship between them varies in different conditions. Structural changes contribute much to the dynamics of their relationship at the canopy scale, whereas the role of physiological mechanisms is not very clear. Here, based on three-year continuous observations from 2018 to 2020 in a maize field in Northwest China, we obtained the total SIF (tSIF) at the photosystem scale and investigated the seasonal dynamics of its link with GPP. Using the ratio of tSIF to GPP, we eliminated the contribution of canopy structure and discovered an increase in the ratio during the late reproductive and ripening stages. Seasonal variation in the ratio was tracked by the leaf chlorophyll contents (LCC) related to the photosynthetic functional maturity (represented by maximum carboxylation rate, Vcmax). In addition, we also found that there was variation in the regression slope of the relationship between SIF/GPP and LCC at different growth stages. The correlation between tSIF/GPP and LCC was better than that between dSIF/GPP (dSIF, the ratio of directional SIF at canopy scale to GPP) and LCC, which demonstrated that the physiological information is reinforced after the elimination of structural contributions. Overall, the seasonal dynamics of the GPP–tSIF relationship in our study highlighted the necessity of considering the growing stage in SIF-based GPP estimations. Although they are usually covered up by the contribution of the canopy structure, physiological mechanisms still impacted the dynamics of the GPP–SIF relationship.