The influence of a stationary shear flow on the crystallization in a glassy system is studied by means of molecular dynamics simulations and subsequent cluster analysis. The results reveal two opposite effects of the shear flow on the processes of topological ordering in the system. Shear promotes the formation of separated crystallites and suppresses the appearance of the large clusters. The shear-induced ordering proceeds in two stages, where the first stage is related mainly to the growth of crystallites and the second stage is due to an adjustment of the created clusters and a progressive alignment of their lattice directions. The influence of strain and shear rate on the crystallization is also investigated. In particular, we find two plausible phenomenological relations between the shear rate and the characteristic time scale needed for ordering of the amorphous system under shear.