The risk associated with human exposure to short-chain chlorinated paraffins (SCCPs) via dietary intake are of great concern because of the bioaccumulation potential of SCCPs in biota and adverse effects. Fish are an important food source for human beings. However, there is a paucity of studies on human exposure to SCCPs via fish consumption. In this study, SCCPs were measured in frequently consumed river fish from the Pearl River Delta, and farmed freshwater fish and wild sea fish from the Yangtze River Delta. Lipid-normalized SCCP levels in river fish ranged from 3000 to 41,000 ng/g lipid weight (lw), with an average of 16,000 ± 12,000 ng/g lw. SCCP concentrations in farmed fish were significantly lower than those in river fish (p < 0.05), but significantly higher than those in sea fish (p < 0.05). Homologue patterns of SCCPs in river fish, farmed fish and sea fish were similar, with CCl SCCPs being the predominant homologues. SCCP concentrations in river fish increased significantly with increasing lipid content (p < 0.01), indicating that lipid content was a controlling factor influencing SCCP concentrations. Body length and weight also played important roles in SCCP concentrations in river fish, as SCCP concentrations decreased with the increase of body length and weight of breams, keeled mullets and tilapias. Although risk assessment implied no significant risk for human exposure to SCCPs via consuming fish collected in this study, the estimated daily intakes indicated that the consumption of sea fish was safer than farmed freshwater fish.