In this paper, a stochastic nonlinear multiscale computational scheme is proposed to study the influence of the variability in both physical parameters of constituent materials and geometrical parameters such as fiber orientation, fiber arrangement of short fiber reinforced composites on the damage propagation. The aim is to predict many probable damage patterns in a huge number of scenarios under complex strain conditions and to discuss the influential level of variability in the physical and geometrical parameters for short fiber reinforced composites. The parameterization and numerical modelling for short fiber reinforced plastics made by injection molding are conducted. The random physical parameters are considered theoretically by the first-order perturbation based stochastic homogenization method, while sampling is used for the random geometrical parameters. When the scenario becomes huge in the stochastic nonlinear analysis, a computational scheme using sub-sampling is proposed. Moreover, the stochastic prediction of the homogenized properties of the composite material and their probable degradation are discussed. The stochastic computation of microscopic strains is analyzed though the damage propagation simulation. When the geometrical variability is considered, a definition of an average strain distribution among many samples is also presented. The efficiency of the accelerated element-by-element scaled conjugate gradient iterative solver is shown by solving many three-dimension random short fiber reinforced models with hundreds of thousands of degrees of freedom. The stochastic computational scheme provides a suitable reference to predict failure under specific reliability requirements of short fiber reinforced composites or other composite materials.