Reconnaissance mission planning of multiple unmanned aerial vehicles (UAVs) under an adversarial environment is a discrete combinatorial optimization problem which is proved to be a non-deterministic polynomial (NP)-complete problem. The purpose of this study is to research intelligent multi-UAVs reconnaissance mission planning and online re-planning algorithm under various constraints in mission areas. For numerous targets scattered in the wide area, a reconnaissance mission planning and re-planning system is established, which includes five modules, including intelligence analysis, sub-mission area division, mission sequence planning, path smoothing, and online re-planning. The intelligence analysis module depicts the attribute of targets and the heterogeneous characteristic of UAVs and computes the number of sub-mission areas on consideration of voyage distance constraints. In the sub-mission area division module, an improved K-means clustering algorithm is designed to divide the reconnaissance mission area into several sub-mission areas, and each sub-mission is detected by the UAV loaded with various detective sensors. To control reconnaissance cost, the sampling and iteration algorithms are proposed in the mission sequence planning module, which are utilized to solve the optimal or approximately optimal reconnaissance sequence. In the path smoothing module, the Dubins curve is applied to smooth the flight path, which assure the availability of the planned path. Furthermore, an online re-planning algorithm is designed for the uncertain factor that the UAV is damaged. Finally, reconnaissance planning and re-planning experiment results show that the algorithm proposed in this paper are effective and the algorithms designed for sequence planning have a great advantage in solving efficiency and optimality.