To date, hepatopancreatic necrosis disease (HPND) in Eriocheir sinensis is causing huge financial losses to the aquaculture industry while the cause of HPND remains unclear. Our previous study has implied that HPND is probably relevant to the damages caused by insecticide residues. In this work, the comparative studies regarding histopathology and trends in immune‐related/detoxifying enzymes activities of the crabs were performed between exposed to the low concentration of insecticides (i.e. β‐cypermethrin 8.52 × 10−12 g/L and trichlorfon 5 × 10−5 g/L) in a long‐term (90‐days) and suffered from HPND. The concentration was obtained by a median‐lethal concentration (LC50) and a safe concentration (SC), and it was 10 times lower than the safe concentration in this experiment. This work's principal aim was to investigate the potential chronic effects of low concentrations of insecticides exposure on crabs and their relevance with HPND. As a result, crabs exposed to the low concentration of insecticides caused similar clinical symptoms and severity in hepatopancreas and other tissue damages like HPND. Meanwhile, catalase (CAT), superoxide dismutase (SOD), malondialdehyde (MDA), acid phosphatase (ACP), alkaline phosphatase (AKP), lysozyme (LZM) and carboxylesterase (CarE) enzymatic activity increased after exposure to the two insecticides and then decreased in the later stages, while the activity of glutathione S‐transferase (GSTs) has barely changed. Results of enzymatic activity indicated that the two insecticides induced oxidative damage to the hepatopancreas of E. sinensis. These evidence indicated that the chronic damage caused by the low concentration of insecticides, which is considered insecticide residue, might be part of the causes of HPND in crabs. The present work may enhance our understanding of the pathogenesis of HPND and provide a theoretical basis for the management of intensive crab aquaculture.