The study has integrated the data from PISA 2006 to 2012 to give an overall picture of the cognitive and affective performances and pedagogy of East Asian regions on PISA scientific literacy. Attempts are made to account for their performances based on the PISA data and cultural characteristics. The cognitive science performance of East Asian regions is definitely very good. On the affective measures, East Asian students tend to have low self concept on learning science, but they generally show high interest in and give high value toward science and science learning except for many students in Japan and Korea. Science teachers in these regions tend to teach more traditionally: fewer hands on activities, less interaction and less emphasis on the application of science. HLM [hierarchical linear modeling] analysis reveal that interaction, hands on activity and investigation seem not much related to good cognitive and affective performances for most East Asian regions, particularly for Japan and Korea. Despite large class sizes, East Asian students are attentive and disciplined in class. Teachers, though demanding and authoritarian in class, get along well with students and are eager to offer help on their learning after class. Despite ordinary class time for learning science, students in East Asian schools often spend lots of time on after-school tutorial classes, which, together with less truancy and greater attentiveness in class, render the actual learning time of East Asian students more. The Confucian culture and the related characteristics of the Chinese learners and teachers are probably the root causes to the performances and characteristics of these East Asian regions.