The micro-regional theory is the product of regional research development under the new situation. The Fergana Valley is a key node in the construction of the BRI；it’s also a typical micro-region. Analyzing the security risks of the Fergana Valley from the perspective of micro-regional research and proposing a governance plan has not only the theoretical significance of enriching the research of micro-region and security governance，but also the practical significance of guaranteeing the construction of the BRI and serving as experience for safety governance of other micro-regions. Currently，the security risks in the Fergana micro-region are complex and diverse，mainly including border disputes，terrorism，political unrest，cross-border crimes，and ethnic conflicts. Security risks present a situation of linkage，which is manifested as a linkage of different types of risks at the intra-micro-regional level，also as a spatial linkage of internal and external risks at the cross-regional level. Under the dual linkage of the security risks，intra-micro-regional governance faces the dilemma of system and capability，and cross-regional governance faces the dilemma of conception and action. In order to optimize governance，at the intra-micro-regional level it is necessary to build a governance mechanism between and within the three countries concerned，and to enhance hard-strike capabilities and soft governance capabilities，and at the cross-regional level，it is necessary to improve the concept of security governance and promote coordination among major powers on the basis of common interests. In the Fergana micro-regional security governance，China must not only actively prevent and resolve the linkage of security risks，but also strive to eliminate its social and economic roots.