The recovery of rare earths from industrial rare earth leaching solution is typically achieved through the ammonium carbonate precipitation method, which presents challenges in terms of prolonged production cycle and ammonia nitrogen pollution. The present study explored the synthesis of crystalline yttrium carbonate in a sodium carbonate system, employing a conventional mother liquor derived from yttrium chloride. The growth of yttrium carbonate was explored through the lens of density functional theory (DFT) calculations, unveiling a novel perspective on its formation mechanism. The synthesized yttrium carbonate demonstrates enhanced crystallinity, with a D50 value of 19.75 μm achieved under reaction conditions comprising a temperature of 60 °C, stirring rate of 200 r/min, feeding rate of 4 mL/min, and aging time of 30 h. The molar ratio for precipitation is set at 1.6:1. The morphology of yttrium carbonate undergoes a transition from needle-like structures to sheet-like formations, ultimately culminating in the formation of spherical aggregates. The variation in surface energy among distinct crystal planes and CO32– configurations within crystal cells accounts for this phenomenon. The DFT calculations unveil a progression of growth and transformation in yttrium carbonate, commencing from a one-dimensional configuration and culminating in a multidimensional morphology.