Earth observation mission planning for the near space aircrafts is a vital problem in the application of near space aircrafts. It plays an important role in satisfying the requirement of earth observation mission most and increasing the utilization rate of aircraft resources. Considering the mission requirement constrains and payload constrains, the paper conceives the mixed integer programming model for earth observation missions of the near space aircrafts firstly, then analyzes the possible conflicts among the earth observation missions, put forwards the conception of possible conflicts of missions and divides up the whole set of missions into the sets of possible conflicts missions using the conception. The paper gives the calculation method of mission executing conflict degree subsequently and designs a genetic and simulated annealing algorithm based on conflicts resolution. At the end the paper proves the validity of the algorithm by the simulation example.