A systematic investigation of the strain distribution of self-organized, lens-shaped quantum dot in the case of growth direction on (001) substrate was presented. The three-dimensional finite element analysis for an array of dots was used for the strain calculation. The dependence of the strain energy density distribution on the thickness of the capping layer was investigated in detail when the elastic characteristics of the matrix material were anisotropic. It is shown that the elastic anisotropic greatly influences the stress, strain, and strain energy density in the quantum dot structures. The anisotropic ratio of the matrix material and the combination with different thicknesses of the capping layer, may lead to different strain energy density minimum locations on the capping layer surface, which can result in various vertical ordering phenomena for the next layer of quantum dots, i.e. partial alignment, random alignment, and complete alignment.