This paper investigate influence of various parameters on the nonlinear behavior of R.C. deep beams. Reinforced Concrete deep beams are one of the structural element that used in dams, offshore piers, rectangular tanks, bridges, floors, diaphragms and high rise buildings. Definition of deep beam by various codes is based on span to height of beam ratio. Generally, span to height ratio of deep beams required not to be greater 2.5. In this paper, three deep beams which have been tested in laboratory already, have been analyzed with various number of element by a nonlinear layered finite element program. In the nonlinear analysis section, results include vertical load versus vertical displacement curve, crack pattern, cracking load and ultimate load. For investigating deep beams behavior, a parametric study used to investigate size–effect phenomenon, tension and compression strength of concrete, yield strength of reinforcement (bar), amount of longitudinal and vertical reinforcement, location and percentage of opening. Also, a new method proposed for placing reinforcement cage in the shear failure area and analytical results compared to experimental results. Results comparison show that nonlinear layered finite element method can be used for investigating of R.C. deep beams with high accuracy.