The invention discloses a preparation method of a spherical microporous niobate molecular sieve fiber. The preparation method comprises the steps of: preparing aqueous alkali with the concentration of 0.5M-2M; weighing niobium pentaoxide powder and measuring the aqueous alkali, respectively adding in a duplex cavity polytetrafluoroethylene inner lining; adding isopropanol in the single cavity of the polytetrafluoroethylene inner lining; keeping the volume ratio of the isopropanol to water at 1:1 and degree of filling at 20%-80%; placing the polytetrafluoroethylene inner lining in a stainless hydrothermal reactor and performing hydrothermal reaction for 2-16h at 180--240 DEG C to obtain sediment; and filtering the sediment to be neutral; and drying for 24-48h at 60-100 DEG C to obtain the spherical microporous niobate molecular sieve fiber. The preparation method is simple in procedures without adding a template and a surfactant; and the obtained dandelion-shaped niobate powder can be used for separating harmful substances in radioactive nuclear waste or polluted water, and has great significance on environmental engineering.