There is growing evidence that recombinant VP28 protein (rVP28) can significantly enhance immune response and disease resistance against white spot syndrome virus (WSSV) in shrimp, although the underlying mechanisms have not been entirely clarified yet. The aim of this study was to determine the effect of rVP28 on histological alterations and WSSV-induced apoptosis in crayfish Procambarus clarkii. Crayfish were fed commercial diets supplemented with different doses of HyNPV-VP28 infected pupae (rVP28-hp) for 4 weeks. Results showed that rVP28-hp may be used as a safe and effective source of medicinal proteins in aquaculture when supplemented in diet at low dose (10 g kg−1 and 50 g kg−1), which could obviously reduce the percentage of apoptotic cells in stomach, gut and hepatopancreas tissues induced by the WSSV challenge and showed the relative percent survival (RPS) of 82.2% and 94.4%, respectively. But rVP28-hp would be detrimental to crayfish survival and decrease resistance to WSSV infection at the high dose (100 g kg−1 and 200 g kg−1), with the cumulative mortality of up to 48.2% and 56.6% after WSSV challenge, respectively. During a 28-d feeding period, the survival rate of crayfish was only 54.5%–75.6%, and histopathological observation showed that one of the principal lesions was serious cell swelling, vacuolar degeneration and necrosis in hepatopancreatic epithelia and myocardial cells. These results suggested that rVP28-hp can influence the immune functions of crayfish in a dose-dependent manner, and the rVP28-hp at the dose of 50 g kg−1 was recommended to prevent WSSV in crayfish culture.