Lecture notetaking is beneficial for learning at different educational levels. However, studies are not in consensus on effective lecture notetaking, and few have investigated the factors influencing it, particularly among secondary school students. This study explored effective lecture notetaking and examined the effects of students’ learning beliefs, learning motivation, and teachers’ instructions on it, by comparing Japanese (n = 340) and Chinese (n = 410) high school students. First, a lecture notetaking scale was obtained of two-factor structure: deep notetaking and shallow notetaking. Then, a multigroup structural equation modeling analysis was performed, illustrating how those factors influence lecture notetaking in the two groups. This study is the first to investigate effective lecture notetaking as a self-regulated strategy to be cultivated; this is an aspect that has been overlooked in past studies. The results indicate that further exploration of teachers’ strategy instructions in school settings is needed in both Japan and China.