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Objective To investigate the anti-fatigue effect and possible mechanisms of micronutrient compound. Methods One hundred and twenty-five male Kunming mice (SPF) were fed following different feeding stuffs: sufficient feed, i.e. AIN-93M feed (corn starch 46.6%, casein 14%, dextrinized corn starch 15.5%, sucrose 10%, soybean oil 4%, fiber 5%, mineral mix 3.5%, vitamin mix 1%, L-cystine 0.18%, choline chloride 0.138% and tert-butylhydroquinone 8 ppm); insufficient feed (composed the same ingredients as the AIN-93M diet, replacing 30%, 50% or 70% of the content of mineral and vitamin mix with corn starch); compound micronutrient-added feed (CMAF, replacing 30% of the content of mineral and vitamin mix of AIN-93M diet with micronutrient compound composed of (g/kg) Vit A 0.25, Vit B1 0.3, Vit B2 0.3, Vit B6 0.35, nicotinic acid 1.5, Vit D 0.05, Vit C 50, Vit E 10, calcium carbonate 180, ferrous glycine 1, zinc lactate 1 and corn starch 755.25). The mice were fed for 14 or 28 d, and then subjected to forced swim test with a load on their tails to exhaustion. The maximal swimming time was recorded. In another experiment, the Kunming mice were fed with corresponding feed for 28 d, and then subjected to forced swim test for 60 min, thereafter the samples of blood and liver were collected immediately. The serum contents of glucose, lactate, nonprotein nitrogen, nonesterified fatty acids and hepatic glycogen were measured. Results The dietary intake of 30% nutritional insufficient group (30% group) was significantly decreased compared with normal control group (fed with AIN-93M diet), (P < 0.05); and there were no significant difference in dietary intake between the two other nutritional insufficient group (50% and 70% group) and normal control group. The swimming time was shorter in three nutritional insufficient groups than in normal control group, (P < 0.05). Compared with nutritional insufficient group, swimming time to exhaustion for mice CMAF were prolonged by 13.2%, however, the difference was not significant, (P > 0.05). The serum glucose and hepatic glycogen decreased and serum lactate, nonprotein nitrogen and nonesterified fatty acids increased in the control group, which were aggravated in nutrient insufficient group and reversed in micronutrient supplementation group. Conclusions Insufficient intake of micronutrients has significant influence on swimming endurance in mice and compound micronutrient supplementation may be of an anti-fatigue effect and improve the endurance of mice with malnutrition during exercise, which may be related to the regulation of energy metabolism during swimming.