In the whole 1990s, having experienced ups and downs, chops and changes, Sino-Japan relations are in a drifting condition without an aim. Territory, Taiwan, textbooks and TMD issues have formed the crux of Sino-Japan stagnated relations in this period. Which are the same or diferences for the basis of Sino- Japan relations in the new century? In the security field, China is vigilant at Japan to be “a military power”, while Japan is worried about “China's threat”, especially Taiwan issue and the deployment of TMD. In keeping Asia's stability and development, both China and Japan are thinking of how to make contributions to Asia's economic development as to form a new basis for the stable development of their bilateral relationship. As to historical understanding, if better dealed with, it could be helpful to improve the friendship between the Chinese and Japanese people. Otherwise, it will play a worse role on undermining the stable development of bilateral relationship. On this issue, economic cooperation will become a powerful backing in Sino-Japan relations and an indispensable factor in carrying out their policy decisions. To well deal with these issues, what counts is to further trust with each other, clear their minds of doubts and make the peoples of two countries better understand each other. Thus, the mass media of two countries should keep calm and cautious, draw a distinction between the government and the people, the overall and layout, the principal and secondary aspects on the relevent reports.