The COVID-19 outbreak has exerted serious effects on the transportation system, especially public transport. Flex route transit (FRT), one of public transport, has shown significant advantages in transporting passengers during COVID-19 due to its high flexibility and relatively large cabin spaces. This study aims to estimate the effects of the lockdown and first lockdown ease on FRT utilization through interrupted time series analysis. A survey was conducted in Beijing to collect data regarding the daily FRT utilization of individuals, spanning from December 2019 to May 2020. Results indicated that FRT utilization was immediately reduced during the lockdown, and a decreased trend was observed. After the first lockdown ease was rolled out, FRT utilization showed a rising level and trend. Private car owners showed a lower dependence on FRT than non-car owners. The level of income exerted varying effects in a wide range of periods. FRT utilization among the higher income group was more likely to take effect than the lower income group. The study yields various policy implications for FRT operations during COVID-19 or other pandemics.