To address the demands of precision agriculture and the measurement of plant photosynthetic response and nitrogen status, it is necessary to employ advanced methods for estimating chlorophyll content quickly and non-destructively at a large scale. Therefore, we explored the utilization of both linear regression and machine learning methodology to improve the prediction of leaf chlorophyll content (LCC) in citrus trees through the analysis of hyperspectral reflectance data in a field experiment. And the relationship between phenology and LCC estimation was also tested in this study. The LCC of citrus tree leaves at five growth seasons (May, June, August, October, and December) were measured alongside measurements of leaf hyperspectral reflectance. The measured LCC data and spectral parameters were used for evaluating LCC using univariate linear regression (ULR), multivariate linear regression (MLR), random forest regression (RFR), K-nearest neighbor regression (KNNR), and support vector regression (SVR). The results revealed the following: the MLR and machine learning models (RFR, KNNR, SVR), in both October and December, performed well in LCC estimation with a coefficient of determination (R2) greater than 0.70. In August, the ULR model performed the best, achieving an R2 of 0.69 and root mean square error (RMSE) of 8.92. However, the RFR model demonstrated the highest predictive power for estimating LCC in May, June, October, and December. Furthermore, the prediction accuracy was the best with the RFR model with parameters VOG2 and Carte4 in October, achieving an R2 of 0.83 and RMSE of 6.67. Our findings revealed that using just a few spectral parameters can efficiently estimate LCC in citrus trees, showing substantial promise for implementation in large-scale orchards.