The "1972 system", which was started in the 1970's by China and Japan, had been experienced rapid development in the 1980's, and the political and economic relations between the two countries showed a good trend. However,in the 1990’s, because of "China Threat Theory", the "1972 system” that maintains the strategic foundation has been shaken. Sino-Japanese relations has experienced" period of wandering”, “period of cooling off",and "period of adjustment”; and it is leading to the “period of confrontation”. With the adjustment and change of the relations between the two countries, the hidden lies in the historical understanding of the problems between the twocountries, the territorial issue, and the Taiwan issue rise to the surface and become a barrier of the development of bilateral relations. At present, the relationship between the two countries has been transforming from the "cooperation in the competition relations" to "competition in the cooperative relations". From the global level, the Sino-US relations are the most important bilateral relations, and the Sino-Japanese relations are the most important bilateral relations at there gional level. Inorder to achieve the benign development of bilateralrelations, China and Japan, should examine the bilateral relations from the perspective and level of strategy, and abide the signed framework of good will between two countries to restore political mutual trust. Region balance and domestic political factors will still be the important variables that affect the normal development of bilateral relations.