The changing of education activities (offline into online) to reduce coronavirus transmission during COVID-19 pandemi has influence on the learning strategies, which ultimately might impact the achievement of learning objectives. Therefore, we conducted a cross-sectional study using a valid (p < 0.01; two-tailed Pearson correlation) and reliable (r = 0.878 and r = 0.849; Cronbach Alpha) online questionnaire to evaluate the perspectives of human anatomy lecturers and undergraduate medical students in Indonesia in implementing the online anatomy learning. We also explored their expectations and preferred learning methods after COVID-19 pandemic. Using purposive sampling, 467 respondents, which consisted of 66 lecturers from 41 universities in six islands (Java, Sumatera, Kalimantan, Sulawesi, Nusa Tenggara and Papua) and 401 students from 19 universities in four islands (Java, Sumatera, Kalimantan, Papua) were recruited. A Chi-square test was used to analyze the differences in categorical variables. The lecturers (74.2%) and students (63.1%) agreed that online learning effectively delivered the course material (p = 0.095). They (69.7% lecturers and 57.9% students) also agreed that learning time allocation was sufficient (p = 0.079); moreover, lecturers (53%) and students (56.1%) had good interaction (p = 0.689). Nevertheless, 56.1% lecturers and 63.3% students had problem during online practical sessions. They had different perspectives about issues during online classes (69.7% vs 36.4%; p < 0.01), motivation improvement (72.7% vs 37.4%; p < 0.01), and time management (87.9% vs 58.4%; p < 0.01). According to the location of the university, especially in the student's side, students in Java had higher proportion in the two aspects, i.e. learning material (p < 0.01) and lecturer-student interaction (p < 0.01), and had lower proportion in the problems during online class (p = 0.003) and practical sessions (p = 0.008). Majority of the respondents (62,2% lecturers in Java, 71.4% lecturers outside Java, 79.6% Students in Java, and 76.6% students outside Java) preferred the use of blended learning after the pandemic (new normal era) and expected to continue the cadaveric practical sessions (82.2% lecturers in Java, 81.0% lecturers outside Java, 91.1% students in Java, and 78.3% students outside Java). In conclusion, the study showed that the satisfaction toward online anatomy learning related to the subject’s role (lecturer or student) and the university region in some aspects.