The utilization of nonlinear differential equations has resulted in remarkable progress across various scientific domains, including physics, biology, ecology, and quantum mechanics. Nonetheless, obtaining multiple solutions for nonlinear differential equations can pose considerable challenges, particularly when it is difficult to find suitable initial guesses. To address this issue, we propose a pioneering approach known as the Companion-Based Multilevel Finite Element Method (CBMFEM). This novel technique efficiently and accurately generates multiple initial guesses for solving nonlinear elliptic semi-linear equations containing polynomial nonlinear terms through the use of finite element methods with conforming elements. As a theoretical foundation of CBMFEM, we present an appropriate and new concept of the isolated solution to the nonlinear elliptic equations with multiple solutions. The newly introduced concept is used to establish the inf-sup condition for the linearized equation around the isolated solution. Furthermore, it is crucially used to derive a theoretical error analysis of finite element methods for nonlinear elliptic equations with multiple solutions. A number of numerical results obtained using CBMFEM are then presented and compared with a traditional method. These not only show the CBMFEM's superiority, but also support our theoretical analysis. Additionally, these results showcase the effectiveness and potential of our proposed method in tackling the challenges associated with multiple solutions in nonlinear differential equations with different types of boundary conditions.