Health misinformation is a serious problem that can cause confusion and risk-taking behaviors, undermining public health efforts. Fact-checking has been highlighted as an effective tool for coping with the challenge of misinformation. However, few studies have examined the factors influencing individuals’ health fact-checking behaviors. Using the comprehensive model of information seeking, we conducted a two-wave panel survey in China during the COVID-19 pandemic and explored the underlying process that might hinder COVID-19 fact-checking. The results showed that risk perception and worry about COVID-19 triggered a negative COVID-19 information-seeking experience, which reduced COVID-19 fact-checking. Moreover, the propensity to trust COVID-19 misinformation played a moderating role, such that negative information-seeking experience had a stronger negative effect on fact-checking behaviors for people with a greater propensity to trust misinformation. This study demonstrates the dark side of cognitive and affective responses to risks and health information-seeking experiences. The findings offer important implications for future health communication initiatives to effectively promote health fact-checking behaviors.