This paper investigates the high accuracy three-dimensional (3D) positioning technology by using ultra-wide-band (UWB) based multi-source fusion algorithm for cooperative unmanned aerial vehicles (UAVs) in hybrid outdoor and indoor scenario. Firstly, the system architecture of cooperative UAVs is proposed, and the core idea is that each UAV can act as either reconnaissance node or positioning anchor through a low-cost integrated communication and positioning module (ICPM), providing an effective cooperative positioning scheme among nodes for drone swarm. Secondly, the UWB-based positioning optimization of two-way is designed. Moreover, a multi-source fusion positioning method is proposed to realize increasing the 3D positioning accuracy and seamless handover. Based on the low-cost prototype system, the real flight experiment results show that both horizontal and vertical positioning accuracy of UAV landing point (1σ) can be better than 30cm; besides, the successful rate of seamless handover is approaching 96% in hybrid complex scene. Furthermore, the multi-source fusion positioning scheme based on cooperative UAVs can be also utilized in some practical applications since the cumulative positioning error is satisfied by sub-meter level.