Abstract Dangerous Paracoccus marginatus papaya mealybugs cause considerable threats and challenges to cassava production and processing. The deployment of resistant cultivars offers effective, economical and eco-friendly management strategies for pest management. We utilized P. marginatus mortality, development and reproduction to evaluate the resistance of fifteen cassava cultivars and conducted physiological and biochemical analyses when P. marginatus was fed on two resistant cultivars (Myanmar, C1115) and three susceptible cultivars (BRA900, Bread, SC205). Significantly lower digestive (amylase, sucrase, lipase), detoxification (glutathione-S-transferase and carboxylesterase) and antioxidant, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and polyphenol oxidase (PPO), enzyme activities were observed in P. marginatus feeding on resistant cultivars compared to susceptible cultivars. For resistant cultivars, a significant reduction was found in nutritional components containing free amino acids, nitrogen, soluble sugars and the secondary metabolite malondialdehyde. Additionally, significantly higher enzymatic activity (SOD, CAT, POD and PPO) levels and secondary metabolite quantities (total phenol and tannins) were found in resistant cultivars induced by P. marginatus compared with susceptible ones. Additionally, RT-qPCR tests showed that the transcripts of ten genes involved in nutrition, secondary metabolites and antioxidant activities were consistent with their physiology and biochemistry changes. Thus, resistant cultivars prevented P. marginatus populations from suffering lower P. marginatus damage by elevating secondary metabolite contents and antioxidant activities, reducing nutrition levels and decreasing enzymatic activities. This study will be beneficial in determining the important indexes for developing standard regulations to evaluate P. marginatus-resistant cassavas, helping the development of effective strategies for pest management.