Female researchers may have experienced more difficulties than their male counterparts since the COVID-19 outbreak because of gendered housework and childcare. To test it, we constructed a unique dataset that connects 15,280,382 scholarly publications and their 11,828,866 authors retrieved from Microsoft Academic Graph data between 2016 and 2020 to various national characteristics from LinkedIn, Johns Hopkins Coronavirus Resource Center, and Covid-19 Community Mobility Reports from Google. Using the dataset, this study estimated how much the proportion of female authors in academic journals on a global scale changed in 2020 (net of recent yearly trends). We observed a decrease in research productivity for female researchers in 2020, mostly as first authors, followed by last author position. We also identified various factors that amplified the gender gap by dividing the authors' backgrounds into individual, organizational and national characteristics. Female researchers were more vulnerable when they were in their mid-career, affiliated to the least influential organizations, and more importantly from less gender-equal countries with higher mortality and restricted mobility as a result of COVID-19. Our findings suggest that female researchers were not necessarily excluded from but were marginalized in research since the COVID-19 outbreak and we discuss its policy implications.