Organic acids are demonstrating outstanding performance in adsorption of heavy metals as a result of their biocompatible and green characteristics, which have attracted widespread attention. In this paper, the extraction rate of citric acid extracts for heavy metals of Cu and Cr in the sludge were investigated. The effects of time, pH, concentration, temperature, and other factors were studied. The results demonstrated that the leaching rate of Cu by citric acid was 82.35% with a reaction time of 18 h, pH 3, solvent concentration of 0.4 mol/L, and reaction temperature of 30 °C. In addition, the leaching rate of Cr was 93.86% at a reaction time of 15 h, pH of 3, solvent concentration of 0.4 mol/L, and reaction temperature of 30 °C. Furthermore, the distribution of environmental heavy metals was evaluated by the BCR three-state continuous extraction method for ionic patterns, which showed that the sludge was leached by citric acid and the heavy metals mainly existed in the exchangeable state and subsequently in the residual state. Eventually, the complexation of citric acid with heavy metal ions was further confirmed by molecular dynamics simulations, which provided an alternative approach and a new perspective for the purification of environmental heavy metals by organic acids.