Quantitative evaluation of stress sensitivity of ultra-deep carbonate reservoirs has been one of the challenges in exploration and development, and the problem of permeability loss law in ultra-deep carbonates under variable stress conditions has not been solved so far and further research is urgently needed. Through experimental and numerical simulation methods, the stress-sensitive evaluation equations were established based on matrix-type carbonate and fractured carbonate reservoirs, the stress-sensitive changes under different Young’s modulus were discussed, and the degree of permeability loss under different stresses was evaluated. Finally, the dual-media model of ultra-deep carbonate was established, and the practical application was carried out in the Shunbei area of the Tarim Basin. Studies have shown that (1) under the same effective stress, the stress sensitivity of matrix-type and fracture-type carbonate reservoirs is related to the Young’s modulus of the rock skeleton. In matrix-type carbonate reservoirs, rocks with a larger Young’s modulus have smaller rigidity and stronger stress sensitivity. In fracture-type carbonate reservoirs, the stress sensitivity is relatively weak under a smaller Young’s modulus, and relatively strong under a larger Young’s modulus. (2) Measured under the conditions of 87 MPa of peripheral pressure, 50 MPa of flow pressure, and 120 °C, the effective stress of matrix-type carbonate reservoirs has an exponential relationship with the permeability of reservoirs. The degree of stress sensitivity for fracture-type is generally higher than that of matrix-type reservoirs, and the smaller the Young’s modulus, the larger the difference in stress sensitivity. (3) The stress sensitivity of typical ultra-deep carbonates in the Shunbei area of the Tarim Basin is higher by establishing a dual-porosity model based on the initiating pressure gradient, which supports new evidence for the characteristics of ultra-deep carbonates with high-stress sensitivity. In actual production, the impact of stress sensitivity on the reservoir volume calculation and efficient development of ultra-deep carbonate reservoirs requires critical attention.