The Chinese government enforced mandatory quarantine for 60 days (from 10 May to 8 July 2009) as a preventative strategy to control the spread of the 2009 H1N1 pandemic. Such a prevention strategy was stricter than other non-pharmaceutical interventions that were carried out in many other countries. We evaluated the effectiveness of the mandatory quarantine and provide suggestions for interventions against possible future influenza pandemics. We selected one city, Beijing, as the analysis target. We reviewed the epidemiologic dynamics of the 2009 H1N1 pandemic and the implementation of quarantine measures in Beijing. The infectious population was simulated under two scenarios (quarantined and not quarantined) using a deterministic Susceptible-Exposed-Infectious-Recovered (SEIR) model. The basic reproduction number R0 was adjusted to match the epidemic wave in Beijing. We found that mandatory quarantine served to postpone the spread of the 2009 H1N1 pandemic in Beijing by one and a half months. If mandatory quarantine was not enforced in Beijing, the infectious population could have reached 1,553 by 21 October, i.e., 5.6 times higher than the observed number. When the cost of quarantine is taken into account, mandatory quarantine was not an economically effective intervention approach against the 2009 H1N1 pandemic. We suggest adopting mitigation methods for an influenza pandemic with low mortality and morbidity.