The invention provides a near space atmosphere environment detector and an operating method thereof. The detector comprises a load grade system and a booster grade system; the booster grade system comprises a rocket body structure, a booster grade control subsystem and a booster grade power mechanism; the booster grade control subsystem is used for detecting the attitude and motion information of the rocket body structure when the load grade system is separated, and then controls the operation of the booster grade power mechanism according to the attitude and motion information of the rocket body structure, and therefore backward-thrust braking is provided to make the rocket body structure land in the vertical direction; the load grade system comprises a payload bay carried with an environment detection instrument, a load grade control subsystem and a load grade power mechanism; the load grade control subsystem is used for controlling the load grade power mechanism to operate in dependence on detected attitude, height, motion and guidance information, control of flying trajectories of the payload bay, the load grade control subsystem and the load grade power mechanism is achieved, and at least two times of skip flying is achieved.