A new thermodevice is developed to measure low-temperature thermal conductivity of organic single crystals that often grow only minute. The technique of Micro Electro Mechanical Systems (MEMS) is employed, so that samples with the length from a few tens to several hundreds of μm can be mounted. Spatially sustained structures of a micro-film heater and resistive thermometer films for the thermal conductivity measurement are fabricated using photolithography processes. To examine the applicability of the thermodevice, the low-temperature thermal conductivity in a submillimeter-sclale rubrene organic semiconductor crystal measured by the MEMS device is compared with that in millimeter-scale crystals of the same compound measured in a conventional method without the microdevice. Reasonable agreement between the two demonstrates the usefulness of the presently developed MEMS thermodevices.