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Abstract Background Influenza vaccinations play an important role in preventing influenza related hospitalizations. The objective of this study was to estimate the effectiveness of vaccination in protecting Beijing residents aged ≥60 years from influenza related hospitalizations during the 2016/17 and 2017/18 influenza seasons. Methods Patients who met the definition of severe acute respiratory infection (SARI) and were hospitalized in the nine sentinel hospitals in Beijing during the 2016/17 and 2017/18 influenza seasons were identified as the study population. The vaccination status of patients was obtained from a vaccination registry. Real-time reverse transcription polymerase chain reaction (RT-PCR) experiments were conducted to test pharyngeal or lower respiratory tract samples collected from SARI patients for influenza A and B viruses. Vaccine effectiveness (VE) was examined using a test-negative design that compare the odds of vaccination among influenza positives and negatives, adjusting for calendar week of illness onset, age, and underlying medical conditions. Results We identified 50,364 patients in the study, in which there were 145 influenza cases and 528 influenza-negative controls aged ≥60 years in 2016/17 season and 149 cases and 358 controls aged ≥60 years in 2017/18 season. The most commonly identified subtype among participants was influenza A(H3N2) in 2016/17 and 2017/18 season (78.5% and 70.6%). Among the adults aged ≥60 years, the adjusted VE of vaccination against any influenza virus for serious acute respiratory infection (SARI) patients was 32.8% (95% confidence interval [CI]: −22.0 to 63.0%) in 2016/17 season. While the adjusted VE in 2017/18 season were 4.6% (95% CI: −72.4 to 47.2%) against any types of influenza, 29.2% (95% CI: −92.9 to 74%) against influenza A(H1N1)pdm09, −37.7% (95% CI: −293.8; 51.9%) against influenza A(H3N2) viruses, and 3.6% (95% CI: −113.8 to 56.5%) against influenza B. Conclusion The influenza vaccine provided moderate protection in 2016/17 season and mild protection in 2017/18 season for influenza related inpatients of adults aged ≥60 years in Beijing. [ABSTRACT FROM AUTHOR]