The impacts of the Mainland China sub-regional economic cooperation strategy to neighboring countries and areas on politics and economy have become more increasingly. This paper specifies the comparisons and estimations of the sub-regional economic cooperation's institutions and the effects of the regions where Mainland China implements the principle of "One Country, Two Systems". In comparison to the institutions of "Guangdong-HongKong-Macau Cooperation Framework" and "Western Taiwan Straits Economic Zone", there is some resemblance and isomorphism between the schemes of the institutions, the contrast and pattern of the operation is obvious. Furthermore, with the order of the implementation, this paper is going to argue the planning and the implementation of the "Western Taiwan Straits Economic Zone" has the references of the "Guangdong-HongKong-Macau Cooperation Framework". In addition, in the evaluation of the effectiveness of the foregoing two sub-regional economic cooperation, the differences between the principal parts of the practices are the key factors why "Guangdong-HongKong-Macau Cooperation Framework" surpasses "Western Taiwan Straits Economic Zone", which is also the requirement of the success of the Mainland China cross-border sub-regional economic cooperation zones.