The invention discloses a method for extracting and separating molybdenum (VI) in an aqueous solution. The method is mainly characterized in that a non-ionic surface active agent, the molybdenum-containing aqueous solution, a saline solution and deionized water are mixed and stirred evenly, the concentration of the non-ionic surface active agent is 50-300 g/L, the concentration of molybdenum is 1-40 g/L, and the salt concentration is 50-300 g/L; the pH value is adjusted to 1-4, the mixture is subjected to still standing and phase separation after being stirred for 10-60 min at 25-80 DEG C, phase separation is conducted for 10-60 min, an aqueous two-phase system with the upper phase being a non-ionic surface active agent phase loading the molybdenum and the lower phase being an aqueous phase, and the concentration of the molybdenum in the non-ionic surface active agent phase loading the molybdenum is 2-80 g/L; the reextraction temperature is 25-80 DEG C, the time is 10-60 min, phase separation is conducted for 10-60 min, the phase ratio of the non-ionic surface active agent phase loading the molybdenum to an ammonium sulfate aqueous solution is 1 to 5, and the reextraction product is ammonium molybdate. According to the method, the extraction rate is high, good phase separation is achieved, the molybdenum extraction rate reaches 95% or above, and the molybdenum reextraction rate reaches 95% or above.