The roots of conflicts of the Great Lakes region of Africa are very sophisticated，which are interwoven with historical and realistic ones，such as bad causes of colonial rule，ethnic conflict，trans-boundary nations and development issue. Under the mediation of the international community，The present situations of the Great lakes region of Africa tends to be alleviated，of which the core issue lies in Eastern DR Congo. Therefore，the issue of Eastern DR Congo is the key of the resolution of the conflicts of the Region. It is noteworthy that the ease of the present situations of the Great Lakes region of Africa is realized by stopping confrontations among the factions，not by eradicating the roots of the regional conflicts. It will bring some uncertainties，such as the evolutions of domestic political situations and bilateral relations，poverty issue，etc. The paper argues that the roots of regional conflicts，such as ethnic issues，trans-boundary nation issues，should be resolved through nation-state building. Therefore，modern state-building is the key for the resolution of the regional conflicts for the long run.