A vehicle-mounted shelter system comprises a transportation vehicle, a shelter and a conformal radiation protection system. The shelter is provided with a large plate type shelter body of a turning-plate type double-expansion structure, and a CT control room and a CT scanning room are arranged inside the shelter. The CT control room is arranged in front of the shelter, and an image acquisition work station, an image processing work station, a medical displayer, a work chair, a film viewing illuminator and a diagnosis report printer are arranged inside the CT control room. The CT scanning room is arranged on the tail portion of the shelter, and a scanning bed, a CT device, a CT shock absorption support, a shelter body separating plate, a control room separating plate and a control room inspection window are arranged inside the CT scanning room. The conformal radiation protection system comprises a plurality of lead plates of different thicknesses, and the lead plates are arranged on the side wall of the shelter. According to the vehicle-mounted shelter system, on the premise of safe radiation protection, the total weight of the shelter is reduced greatly, the medical service capacity of the shelter is good, the maneuverability is good, and the cost is lowered.