Nickel-based superalloy DD6 is characterized by high strength, high temperature resistance, which makes it an ideal material for manufacturing aircraft engines. Ultrasonic assisted drilling is an advanced machining method, which greatly improves the machining performance of difficult-to-machine materials. The drilling thrust force has an important effect on the hole surface quality, burr height and bit wear. Therefore, it is necessary to predict the thrust force of ultrasonic assisted drilling. However, there are few reports about the thrust force modeling of ultrasonic assisted micro hole drilling. A thrust force prediction model for ultrasonic assisted micro-drilling is presented in this paper. Based on the basic cutting principle, the dynamic cutting thickness, dynamic cutting speed and acoustic softening effect caused by ultrasonic vibration are considered in this model. The model was verified by the ultrasonic assisted drilling experiments with different spindle speeds, feed rates, amplitudes and frequencies. The maximum error and minimum error of the average thrust force are 10.5% and 2.3%, respectively.