The embodiment of the invention provides a micro electro mechanical system mass flow sensor assembly and a manufacturing method thereof. The micro electro mechanical system mass flow sensor assembly comprises a sensor chip and a carrier. The sensor chip comprises a substrate, a supporting film, a thermistor, at least two sensing elements, a heater, a through hole, a conducting layer and a passivation layer. The supporting film and the thermistor are arranged on the first surface of the substrate. The at least two sensing elements and the heater are arranged on the supporting film. The through hole is formed in one end of the substrate and penetrates into a second surface opposite to a first surface from the first surface, and a back contact of the sensor chip is arranged on one side of filler of the through hole. The conducing layer covers the sensing elements, the heater and the thermistor to enable the sensing elements, the heater and the thermistor to be connected to the filler of the through hole, and the passivation layer covers the upper surface of the sensor chip. The carrier is connected with the back contact of the sensor chip through a bonding pad.