The present study investigates the effect of low concentrations of boron on the crystallization of lithium carbonate (Li2CO3). Experimental results indicate that the boron in brine mainly exists in the forms of boric acid (B(OH)3) and borate anion (B(OH)4−). Temperature and pH are critical factors to adjust the ratio of B(OH)3 and B(OH)4−. Meanwhile, the density functional theory calculation results suggest that the interaction of B(OH)4− with Li+ is stronger than that of B(OH)3 with Li+. Based on this result, the effect of boron on the crystallization of Li2CO3 is investigated and discussed at different added forms of boron, added amount of sodium hydroxide, temperatures, and concentrations of boron. B(OH)4− is proved to be the form of boron that has significant influence. Temperature and amount of sodium hydroxide have significant influence on the balance of B(OH)3 and B(OH)4−. The boron content of Li2CO3 significantly decreases as the temperature increases, and that at 80 °C is 133 ppm while that at 25 °C is 397 ppm. And that increases as nNaOH/nB increases. Finally, effect of addition of polyhydric alcohols on reducing boron entrainment is investigated.