This study aims to evaluate acceptance of COVID-19 vaccines and the impact of risk perception on vaccine acceptance and personal health protective behaviors in Taiwan. A nationwide cross-sectional study was conducted from 19 to 30 October 2020; 1020 participants were included in the final analysis; chi-square and logistic regression analyses were conducted. In total, 52.7% of participants were willing to receive COVID-19 vaccines, 63.5% perceived the severity of COVID-19 in Taiwan as “not serious”, and nearly 40% were worried about COVID-19 infection. Participants with higher perceived severity of COVID-19 had significantly higher odds of refusing the vaccine (OR = 1.546), while those worried about infection had lower odds of poor health protective behaviors (OR = 0.685). Vaccine refusal reasons included “the EUA process is not strict enough” (48.7%) and “side effects” (30.3%). Those who had previously refused other vaccinations were 2.44 times more likely to refuse the COVID-19 vaccines. Participants’ age had an influence on COVID-19 vaccine acceptance. In general, the Taiwanese public’s acceptance of the vaccine was lower than that in other high-income countries. Elderly participants and those with college-level education and above who had previously refused vaccines had lower willingness to receive a COVID-19 vaccine. Risk perception was positively associated with personal health protective behaviors but negatively associated with COVID-19 vaccine acceptance.