Emotional intelligence is a main area in educational psychology and a key factor in the academic life of students. It deals with deviant behavior through self-awareness and self-motivation, regulates emotional and social skills, and converts emotional energy into positive energy. This study examined direct and indirect relationships between emotional intelligence and study habits in blended learning environments. Blended learning is conceptualized as a hybrid learning approach that combines online learning opportunities and the traditional classroom approach. Furthermore, the study explored the mediating role of cognitive engagement in the relationship between emotional intelligence and study habits. We used 26 items in a paper-based questionnaire in a quantitative study to collect data on emotional intelligence, cognitive engagement and study habits from health sciences students (N = 338) enrolled in blended learning courses in universities in the Hunan province of China. Emotional intelligence included self-awareness, self-motivation, and the regulation of emotion; social skills were also examined. A partial least squares structural-equation modeling approach was applied through SmartPLS software to explore the relationships. The results indicate that self-awareness and self-motivation have direct, significant, and positive connections with study habits. Similarly, the results indicate that all four dimensions of emotional intelligence (self-awareness, self-motivation, emotion regulation and social skills) had indirect, significant, and positive relationships with study habits using cognitive engagement as a mediator variable. It was concluded that students face higher-than-usual challenges in building study habits in blended learning environments during the COVID-19 pandemic, and that emotional intelligence helps them to develop their study habits to greater effect. Similarly, it was concluded that cognitive engagement strengthens the connection between emotional intelligence and study habits. Therefore, it is recommended that universities take specific measures to enhance students’ emotional intelligence and cognitive engagement, which will ultimately improve their study habits. Moreover, valuable and practical implications for teachers, practitioners, and university management were also discussed in the study.