A liquid-phase single-stage synthesis of isoprene from methyl tert-butyl ether (MTBE) and formalin using Keggin-type heteropolyacids, phosphotungstic acid (PTA), phosphomolybdic acid (PMA), and silicotungstic acid (STA) was performed in a batch reactor. The effects of catalyst concentration, reaction temperature, MTBE/formaldehyde ratio, and solvent type on isoprene yield were evaluated. At moderate reaction conditions, the two-phase organic−aqueous system with cyclohexane addition and high MTBE/formaldehyde ratio enhanced the isoprene formation. When the catalyst concentration was increased, the formaldehyde conversion and turnover frequency increased, but isoprene selectivity slightly decreased. At high temperature or low MTBE/formaldehyde ratio, isoprene yield decreased because of the formation of 3,4-dihydro-4-methyl-2H-pyran. When the catalyst activities are compared, the STA catalyst exhibited formaldehyde conversion, isoprene yield, and selectivity that were slightly higher than those of the PTA and PMA catalysts. Among the Prins reaction products formed, 4,4-dimethyl-1,3-dioxane was the key precursor of isoprene formation in the two-phase reaction system.