The thread connection’s root fillet radius of 0.038″ size is the greatest weakness of the API NC type joints and thread. During the slimehole drilling, especially in the deep and ultra-deep gas well, its stress concentration factor and notch sensitivity factor are very high A novel thread connection design (TM) of a drilling tool is proposed to decrease the fatigue failure of the slimehole drilling tool in the deep and the ultra-deep gas well in the Tarim oilfield China. The novelty in the TM thread structure is, reducing the threads per inch, extending the distance from the last engaged thread to the external shoulder of the pin and adding three threads to the conventional connection. The novel thread connection will improve the slimehole drilling tool’s anti-fatigue life due to its improved elasticity and rigidity. Furthermore, the TM can transfer the maximum stress at the connection root to the loaded surface, which can effectively lower the fatigue notch’s sensitivity coefficient. In this paper, the finite element method (FEM) is applied to carry out the detailed comparative analysis of the TM with existing thread connection NC38, TX60 and TH90. The TM has the lowest stress concentration factor and fatigue notch sensitivity coefficient, so its anti-fatigue life is the highest. In addition, TM is manufactured and is tested at Tarim oilfield in China.