As a precursor phase, amorphous calcium carbonate (ACC) plays a key role in the formation of CaCO3 biominerals, but the detailed information about the structure evolution during the crystallization process of ACC is limited. Herein, based on the confined environment in microfluidics, we have demonstrated a strategy to investigate the crystallization processes of ACC. The characteristics of a confined environment in microfluidics were analyzed through COMSOL Multi physics simulations. By mixing equimolar CaCl2 and Na2CO3 aqueous solutions directly, the reactive crystallization of CaCO3 was monitored on chip by online microscope observation and micro Raman spectroscopy scanning. Combined with offline scanning electron microscopy characterization, we showed that branched aggregate ACC(I) precipitated first once mixing reactant solutions, then the more ordered and whiskerlike ACC(II) was an unexpected result. These whiskerlike ACC(II) either gradually transformed to spherical structure nanocrystalline, vaterite was then formed from it through spherulitic growth mechanism, or the initial rhombohedral crystallographic calcite was formed from whiskerlike ACC(II), then the complete rhombohedral calcite crystals formed through the dissolution/recrystallization of ACC(II). Our results showed an intuition-based way to directly observe the structure evolution of ACC crystallization in the confined environment; it could be of inspiration for the understanding of biomineralization processes.