Higher education attainment is a focus of gender differences research. However, little is known about differences in university students’ major choices at the same level of higher education in China’s education hierarchy. Based on a web survey of 1164 undergraduate students in China’s broad enrollment context, this study uses Wenjuanxing to collect information by posting questionnaires on social media platforms and analyzes the impact of gender differences on the major choices of finance and economics undergraduates by using the Linear Discriminant Model (LDM). Moreover, this study explores the differential impact of income level, urban–rural settings, and regional differences on university students’ major choices. This study finds that female students are approximately 2.62 times more likely than male students to choose applied majors (such as accounting, financial management, auditing, international business, and so on), a gap that is more pronounced in high-income families and Eastern regions. In addition, in rural areas, female students have a higher probability of choosing applied majors than male students. These findings indicate that in China’s broad discipline enrollment model, gender differences still significantly affect students’ major choices, and female students are more likely to enter applied majors than their male counterparts.