Objective: To analyze the changes and related factors of influenza vaccine hesitancy among college students in Shanghai from 2022 to 2025, so as to provide evidence for influenza prevention and control in universities. Methods: A stratified random cluster sampling method was used to select 1 393 college students from Shanghai universities for electronic questionnaire surveys in June 2022 and January to February 2025. The survey mainly included influenza vaccination status, sources of vaccine related information, and potential related factors. Data were analyzed using the Chi-square test, Mann-Whitney U test, and binary Logistic regression. Results: The influenza vaccine hesitancy rate among college students in Shanghai was higher in 2025 ( 40.63 %) than in 2022 (31.95%) ( χ 2=22.73), and the hesitancy score [2022:0 (0,5);2025:0 (0,5)] also increased ( Z = -4.16 ) (both P <0.01). The proportion of students exposed to reports of vaccine adverse events rose from 36.90% in 2022 to 59.22 % in 2025 ( χ 2=139.08, P <0.01). Binary Logistic regression analysis showed that basic influenza knowledge (2022: OR = 0.79 , 95% CI =0.68-0.92; 2025: OR =0.79, 95% CI =0.69-0.90) and previous self paid vaccination with other vaccines (2022: OR =0.52, 95% CI =0.37-0.75; 2025: OR =0.63, 95% CI =0.48-0.83) were associated with influenza vaccine hesitancy among college students in both years; medical professional background ( OR =0.34, 95% CI =0.17-0.67) and trust in healthcare providers recommendations ( OR =0.31, 95% CI =0.11-0.86) were associated with influenza vaccine hesitancy among college students in 2025 (all P <0.05). Conclusions The phenomenon of influenza vaccine hesitancy among college students in Shanghai has intensified. Increased knowledge has failed to offset concerns arising from exposure to negative information. Medical background and recommendations from healthcare providers have become new related factors.