Our aims were to assess the incidence of birthweight discordance of twins, to explore risk factors and its impact on perinatal mortality, and to quantify the risks at different severity of birthweight discordance in Japan, by using a nationwide obstetric database. There were 10,828 pairs of twins, born from 2001 to 2005 recorded in the database of the national Perinatal Health Care Project, fully enrolled. The overall incidence of birthweight discordance was 47.34%. The incidence of mild, severe and extremely severe discordance was 19.26%, 10.21% and 17.87%, respectively. The incidence of birthweight discordance in Japan is much higher than that in other countries, particularly at higher severity level. By linear regression model, our study added independent factors of primiparity (p < .001), sex composition (p < .001), chorionicity (p < .001), gestational age (p < .001), and delivery mode (p < .001) in determining birthweight discordance percentage. Maternal age and application of assisted reproduction technologies (ART) didn't significantly influence the birthweight discordance. The birthweight discordance is closely associated with gestational age and affected discharge mortality. From 25% of birthweight discordance, risk to discharge mortality tended to significantly increase, suggesting it should be added as a reference for clinical practices.