The invention provides a method for smelting molybdenum-vanadium alloy steel through fractional reduction. The method comprises the following steps that (A) an isolation device is inserted into a steel ladle, and a reduction reaction area is built in the isolation device; (B) after a molybdenum carbon block and a vanadium carbon block are added into the reduction reaction area for a fusion reaction, a molybdenum silicon block and a vanadium silicon block are added for a fusion reaction to form molybdenum-vanadium slag; and (C) the molybdenum-vanadium slag is subjected to silicon reduction andaluminum reduction in sequence. According to the method, the consumption of active metal can be reduced, acid slag is avoided, adverse reactions with basic slag and a basic lining in the steel ladle are further avoided, and good effects are realized. When the method is adopted to smelt the molybdenum-vanadium alloy steel, the molybdenum yield is more than 97.5%, and the vanadium yield is more than93.0%. The method is highly worthy of being applied and popularized widely.