Chlorophyll fluorescence has become a very powerful technique to estimate the photosynthetic capacities of different plants in a rapid and non-invasive way. However, the effect of environmental factors on the diurnal variations in chlorophyll fluorescence parameters in different seasons has been less studied, and their relation to vegetation productivity has hardly been discussed. In this study, we characterized the diurnal changes in fluorescence parameters (photochemical efficiency of PSⅡ and non-photochemical quenching (NPQ)), and quantified the influence of the three environmental factors (photosynthetically active radiation (PAR), leaf temperature (T_leaf), and relative humidity (RH) using Boosted Regression Trees (BRT) and Pearson correlation analysis). In addition, the relationships between the fluorescence parameters and vegetation productivity (gross primary productivity (GPP) and light use efficiency (LUE)) were explored. We conducted in situ chlorophyll fluorescence measurements on Slash Pine (Pinus elliottii Engelm.) and Masson Pine (Pinus massoniana Lamb.) in the Qianyanzhou (QYZ) subtropical coniferous plantation, Jiangxi province, China, during 2016. Our results showed that Φ_PSⅡ decreased to a minimum at midday and subsequently progressively rose, whereas NPQ was highest at midday, significantly contrary to Φ_PSⅡ. Among the three environmental factors, PAR played the strongest role in determining the diurnal changes of Φ_PSⅡ (83.0% in Slash Pine and 51.1% in Masson Pine). Φ_PSⅡ decreased with PAR. PAR also had an important influence on NPQ in Slash Pine (77.2%). However, NPQ in Masson Pine was mainly affected by T_leaf (59.6%). In addition, we obtained the synchronous LUE and GPP from the eddy covariance flux observation in QYZ and found that GPP had a significantly negative correlation with Φ_PSⅡ, but a positive correlation with NPQ. LUE increased with Φ_PSⅡ, but sometimes high Φ_PSⅡ was accompanied by low LUE. LUE decreased with NPQ, indicating that higher proportion of heat dissipation resulting in lower light use efficiency.