The process of altering the microbial-induced carbonate precipitation (MICP) by adding additives has been extensively studied. The impact of polysaccharides, as an important component of bacteria, still requires deeper exploration on MICP. This work thus focuses on two types of sugars, sodium alginate (SA) and trehalose (Tre), to explore their effects on biomineralization of carbonate induced by Bacillus pumilus Z6. The results show that B. pumilus Z6 can raise the environmental pH and increase the supersaturation of carbonate and bicarbonate ions through carbonic anhydrase. The presence of organic functional groups and the negative carbon isotope signatures in minerals provide evidence of microbial involvement. Tre and SA do not change the mineral phase, which mainly consists of hollow rice-like granular vaterite and irregular calcite. Tre is conducive to the formation of calcite, whereas the carboxyl groups in SA contribute to the stability of vaterite. Both Tre and SA enhance the removal rate of calcium ions; however, SA is more effective for this purpose. Furthermore, mineralization experiments with calcium alginate gel tablets indicate that SA can attract calcium carbonate to nucleate on its surface. This research offers significant insights into biomineralization processes and introduces novel perspectives for advancing MICP technology.