Anti‐ambipolar transistors (AATs) featuring heterojunctions of n‐ and p‐type semiconductors have garnered significant research interest owing to their unique electrical characteristics. With the nonlinear current response, AATs hold great promise for a wide range of next‐generation electronic applications, further enhancing advanced logic and in‐memory computing functionality. However, the seamless integration of AATs into these applications hinges upon addressing their susceptibility to temperature and bias instabilities, a challenge that has yet to be systematically explored. Here, the origin of these instabilities is reported in AATs composed of indium‐gallium‐zinc oxide (IGZO) and dinaphtho[2,3‐b:2′,3′‐fjthieno[3,2‐b]thiophene (DNTT) through low‐frequency noise (LFN) spectroscopy. The findings reveal that the AATs exhibit a notable reduction in peak current with temperature instability and an abrupt decrease in drain current under applied DC bias. It is examined that these instabilities stem from defect‐related carrier transport mechanisms at the n/p heterojunction, evidenced by the observation of 1/f 4 noise. Furthermore, a comprehensive comparative analysis is provided of 1/f 4 noise behavior with and without the insertion of an insulative layer of AAT. This provides the microscopic origin of how the LFN generation mechanism changes the defect‐related carrier conduction at the interface and mitigates the bias and temperature instabilities.