Total organic carbon (TOC) content and hydrogen index (HI) are critical parameters for evaluating the hydrocarbon generation potential of source rocks and shale gas resources. However, for overmature shales, laboratory-measured residual TOC content and residual HI fail to reflect original properties. In this study, overmature Upper Ordovician to early Silurian Wufeng–Longmaxi shales from south China were selected to estimate the original TOC content and original HI based on major- and trace-element concentrations that are rarely lost during thermal alteration. Proxies were used, including biogenic silica, Cu/Al, P/Al, Mo-enrichment factor (EF), U/Th, U-EF, Al, and Ti content to document the organic matter accumulation process of the Wufeng–Longmaxi Formations. The relationships among proxies for paleoproductivity (biogenic silica), paleoredox conditions (Mo-EF), terrigenous influx (Al), and TOC content suggest that organic matter accumulation was primarily controlled by high paleoproductivity and anoxic conditions. Moreover, the ratio of biogenic silica to total silica is an effective proxy for estimating the marine organic matter fraction. The original HI values of global immature marine shales display a normal distribution; hence, the calculated marine organic matter fraction is hypothesized to conform to a normal distribution. Based on intervals (μ − σ, μ + σ) and (μ − 2σ, μ + 2σ) (μ is the deviation and σ is the variance) with the same probability, a correlation between original HI and organic matter abundance was established. The average restored original TOC and HI were 4.9 wt. % and 493 mg/g, respectively, indicating the dominance of organic matter type I–II1. The thermal maturity and hydrocarbon generation history modeling results suggest that the estimated original TOC and HI values are reasonable.