The invention relates to a movable multifunctional module thermal desorption system. Equipment of the system is divided into three modules; the module I comprises a thermal desorption rotary kiln 1; the module II comprises a cyclone dust collector 2, a secondary combustion chamber 3, a heat exchanger 4, a spray cooling tower 5, an alkali absorption tower 7, an automatic control system 13 and a steam-water separator 14; the module III comprises a bag type dust collector 6, an activated carbon absorber 8, a biofilter 9, an induced draft fan 10, an exhaust device 11 and a booster fan 12; the equipment of the module I, the module II and the module III are respectively arranged on movable equipment. The system is suitable for four process routes including high-concentration and high-toxicity organic compound contaminated sites, general volatile/semi-volatile organic compound contaminated sites, acidic organic compound contaminated sites and organic sulfide and ammonia-nitrogen organic compound contaminated sites; different process routes and equipment can be accurately and effectively provided according to different organic compound contaminated sites, so that the time for designing a technical route is reduced, and the transportation and onsite loading and unloading are convenient.