In the modern foundation pit engineering, pits-in-pits is becoming more and more popular. It needs special analysis according to the structural design requirements of retaining walls. There exists mutual influence between the outer retaining walls and the inner retaining walls; so the stress analysis of the retaining walls is more complicated. For the complex stress condition of the outer and the inner retaining walls in pits-in-pits, a combined bars FEM system based on the flexibility fulcrum method is developed. By solving the spring stiffness of the finite soil mass between the inner and outer retaining walls, the model can be used to solve the problem of calculating the internal force and deformation of the retaining wall. The pits-in-pits case study shows that the deformation and internal force of the retaining structure calculated by flexibility fulcrum method are quite consistent with the engineering practice. The research results have certain theoretical and engineering practical significance.