Soil–rock binary structure slopes are a unique and common phenomenon in water conservancy and geotechnical engineering, with complex stability issues that challenge traditional evaluation methods. This paper proposes the Partitioned Rigid Element–Interface Element–Finite Element (PRE-IE-FE) method, a novel numerical technique that addresses computational efficiency and accuracy in slope stability analysis. The method integrates composite destabilization modes along the soil interior, soil–rock contact surface, and rock structural surfaces, ensuring high computational performance. A slope instability criterion for PRE-IE-FE is established through derived control equations, a developed calculation program, and the strength reduction method. Case studies validate the method’s effectiveness and practicality, offering innovative solutions for similar engineering challenges.