The feature that devices based on blue phase liquid crystals (BPLCs) is free of alignment layers. However, the alignment layers could affect the morphologies of BPLC-devices as well as the electro-optical properties. In this paper, we investigate the influence of alignment layers to crystal growth of polymer-stabilized blue phase liquid crystals (PS-BPLCs). Without alignment layer, PS-BPLCs experiences both homogeneous nucleation and heterogeneous nucleation, and the morphology appears in random crystal orientations. On the contrary, when the surfaces coated with alignment layers, a heterogeneous nucleation dominates during the crystal growth process. We further proposed a possible mechanism for crystal growth under different surface condition. This study provides an alternative method to control crystal growth of PS-BPLCs, which is for facilitating many PS-BPLCs based photonic devices.