Hydrogen Index (HI) is an important parameter for organic matter evaluation. It represents the relative abundance of aliphatic macromolecular hydrocarbons to total organic matter and can be used to reconstruct the history of primary productivity. In order to assessment the reliability of HI as environmental indicator, several sediment cores from three subtropical reservoirs were collected and then analyzed by a combination of Rock-Eval pyrolysis and biomarker analysis (neutral sugars). The historical change of primary productivity in the three reservoirs was also rebuilt by using the HI values and total carbohydrate contents coupled with the ~(210)Pb and ~(137)Cs dating. The result shows that the sedimentary organic matter in ZT and LA reservoirs is mainly derived from planktonic algae and to some extent degraded, whereas that in XFJ reservoir is affected by higher degradation and/or higher plant input at the lower layers of the sediment core. The increasing HI values at each of the three reservoirs are positively correlated with the total carbohydrate contents and the five-year average moving temperature during the recent 50 years, suggesting that the primary productivity in these reservoirs has increased due to climatic change. Meanwhile, the increasing primary productivity has enhanced the accumulation of heavy metals or polycyclic aromatic hydrocarbons in the investigated reservoir sediments.