Sulfonated and fluorescent polymethylsiloxanes (SO3H-PMS) were synthesized, and their effect as additives on in vitro calcium oxalate (CaOx) crystallization was evaluated. SO3H-PMS was prepared by hydrosilylation and sulfonation reactions with poly(dimethylsiloxane-co-hydrogenmethylsiloxane) (PDMS-co-PMHS). Several analytical tools were used to investigate the morphology, crystal structure, and chemical contents of the harvested CaOx crystals. Varying the concentration of SO3H-PMS induces a transition of CaOx monohydrate (COM) with expanded multilayer and circular stacked-sheet morphologies as well as of the bipyramidal CaOx dihydrate (COD) crystals in three crystallization procedures. Energy-dispersive X-ray spectroscopy (EDS) and XRD allowed detecting the presence of Si (0.2–1.0°wt.-%), which stems from SO3H-PMS adsorbed on CaOx, and the selective formation of phases of COM and COD. We demonstrated that the presence of anionic moieties on the SO3H-PMS backbone and their concentration were crucial to control the crystal type, morphology, crystal size, and chemical composition.