In-depth understanding of microstructure development is required to fabricate high quality products by additive manufacturing (for example, 3D printing). Here we report the governing role of side-branching in the microstructure development of alloys by laser powder bed fusion. We show that perturbations on the sides of cells (or dendrites) facilitate crystals to change growth direction by side-branching along orthogonal directions in response to changes in local heat flux. While the continuous epitaxial growth is responsible for slender columnar grains confined to the centreline of melt pools, side-branching frequently happening on the sides of melt pools enables crystals to follow drastic changes in thermal gradient across adjacent melt pools, resulting in substantial broadening of grains. The variation of scan pattern can interrupt the vertical columnar microstructure, but promotes both in-layer and out-of-layer side-branching, in particular resulting in the helical growth of microstructure in a chessboard strategy with 67° rotation between layers.