Remote sensing of solar-induced chlorophyll fluorescence (SIF) provides great potential for estimating gross primary production (GPP) of terrestrial ecosystems. A strong relationship between SIF and GPP has been observed at the seasonal scale from both ground-based and satellite observations. However, variations of SIF due to changes in plant growth stages appear to influence the SIF-GPP relationship. It remains unclear how this relationship is affected by plant growth-related changes, especially for C4 plants such as maize. In this study, continuous in situ measurements for canopy far-red SIF retrieval and GPP calculation were made in maize during the growing season of 2017. Diurnal and seasonal variations of canopy SIF and its yield (SIFyield) were analyzed over different growth stages of maize to understand how they affect the relationship with GPP. The results show that the relationship between SIF and GPP varies with the growth stages of maize during the growing season, indicating that canopy structure has a strong impact on the seasonal variations of canopy SIF and its relation to GPP. Furthermore, we found that SIFyield is significantly correlated with canopy photosynthetic light use efficiency (LUE) at the canopy level throughout the season. However, it is almost uncorrelated with LUE after adjusting for the effects of canopy structure with the structural vegetation index MTVI2. This finding highlights the importance of canopy structure in the relationship between SIFyield and LUE, complicating the use of canopy SIF for tracking vegetation physiological activity. Overall, our observation-based findings show that canopy structure affects the SIF-GPP relationship, strengthening our understanding of the mechanistic link between SIF and photosynthesis.