Purpose: To analyze the occurrence of frequently-occurring diseases among freshmen during military training in colleges and universities, explore the occurrence patterns of various diseases and formulate targeted prevention measures, and also incorporate relevant content on patient psychological support to improve the intervention system. Methods: Freshmen who participated in the 12-day military training in our college in September 2022, September 2023, September 2024, and September 2025 were selected as the research subjects. The four-year sample numbers were 2282, 2453, 2516, and 2217 respectively. The number and incidence of common diseases during the military training were counted, the causes of the disease were analyzed, and preventive countermeasures and psychological support measures were proposed. Results: The total incidence rate of multiple diseases during the four-year military training for freshmen was 18.36%, among which the highest incidence rate of upper respiratory tract infection was 5.28%. The overall incidence rate will be the highest in 2024 and the lowest in 2025. The incidence of trauma and heat stroke among male freshman is higher than that among females (p < 0.05); dysmenorrhea is common among female freshman, whereas no such cases in male freshmen due to their physiological characteristics; there is no significant difference in the incidence rates of other diseases between genders (p > 0.05). Conclusion: The incidence of multiple diseases during the military training of college freshmen is affected by various factors such as environment, physical fitness, and protective measures. Comprehensive intervention such as improving prevention mechanisms, strengthening health education, implementing protective measures, and strengthening psychological support can effectively reduce the incidence of multiple diseases and ensure the physical and mental health of freshmen during military training.