Although the measurement of short-chain chlorinated paraffins (SCCPs) in aquatic ecosystems has increased, limited information is available on their toxic effects on aquatic animals. To evaluate the harmful effects of SCCPs, we assessed their acute impact on 24-h survival and biochemical parameters, as well as their chronic effects on growth and reproduction over three generations in the harpacticoid copepod Tigriopus japonicus. Dose-dependent increases in mortality were observed, with an LC50 value of 74.6 μg L−1 for 24 h. Acute exposure to the LC10 value for 24 h significantly reduced feeding behavior, accompanied by a notable decrease in acetylcholinesterase enzymatic activity. Simultaneously, the intracellular levels of reactive oxygen species increased, along with elevated malondialdehyde contents. Glutathione level was increased by the LC10 value of SCCPs with the induction of enzymatic activities of antioxidant defense components, including glutathione S-transferase, catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase. When T. japonicus was continuously exposed to 1/10 of the NOEC and NOEC values for 12 days across three generations (F0–F2), growth retardation was observed in the F2 generation, with delay in the developmental periods from nauplius to adult. Although the total number of nauplii per brood was not significantly altered across generations, a significant delay in the onset of reproduction was observed in the F2 generation. Our findings suggest that even sublethal concentrations of SCCPs can negatively affect the health of copepod populations with consistent exposure.