Students' preferences and engagement with online educational resources and activities are crucial for academic success in the context of online medical education. This study investigated the preferences of Chinese medical students regarding the teaching strategies used by instructors and their relationship with course difficulty level, student's academic performance, and perceived effectiveness. Survey data (n = 375) were collected from the medical students from one of the largest medical schools in Southern China during the spring semester of 2020. First, exploratory factor analysis demonstrated that there were three latent factors behind online teaching strategies, including teacher-led instructional strategies, supervised and monitored learning strategies, and self-directed learning strategies. Instructional activities under teacher supervision and monitoring received the highest rating while teacher-led strategies received the lowest ratings. Second, the popularity of the three online instructional strategies we have identified was positively associated with students' perceived effectiveness of online teaching and their self-reported academic performance. Third, analysis of the quantified answers to the open-ended question reported a positive association between the perceived difficulty level of the courses and students' preference of teacher-led strategies. It also manifested a positive correlation between perceived effectiveness level of the online teaching and the use of self-directed learning strategies before their online lectures. Further implications of the findings are fully discussed.