It’s important to improve the sealing performance of the inner packer in deepwater pipelines, which is an emergency sealing and oil control equipment. The deformation characteristics and sealing stress conditions of the packer’s sealant cylinder are analyzed, and the hyperelastic constitutive model is determined based on uniaxial tensile experiments. The effective contact stress and effective contact range between the rubber cylinder and the pipe wall are the main parameters for evaluating the sealing performance. Through simulation, it was found that the rubber cylinder on the force application side plays a major sealing role, and severe stress can lead to shoulder protrusions. The location of fatigue damage on the rubber cylinder’s shoulder is consistent with the sea trial. Therefore, special-shaped rubber cylinders with different structures are designed to address the shoulder protrusion. The simulation shows that the sealing performance of the right-angled trapezoidal double-layer rubber cylinder with force applied on the slope side(S-RARC) is significantly better than the original rubber cylinder(ORC), and it does not produce shoulder protrusions.