The invention relates to a method for controlling the contents of phosphorus, sulfur and hydrogen in molten steel. The method comprises the following steps: performing molten iron pretreatment with a knotted reactor (KR) to desulphurize; placing the desulphurized molten iron in a dephosphorization converter to dephosphorize; placing the dephosphorized molten iron in a decarburization converter to smelt; tapping from the decarburization converter, adding ferroaluminum to deoxidize, and adding slag to adjust the slag basicity; and performing Ruhrstahl-Heraeus (RH) refinement. In the method for controlling the contents of phosphorus, sulfur and hydrogen in molten steel, molten iron pretreatment for desulfurization and dephosphorization are adopted, and waste steel which has low sulfur content and is easy to melt is used, thus P is no more than 60ppm and S is no more than 100ppm in the endpoint of the converter; the dosages of aluminum and slag and the addition time are controlled in the topping process of the converter to realize the effects of slag washing and desulfurization and ensure that P is no more than 80ppm and S is no more than 60ppm in the RH refinement; and after RH refinement is performed to degas and refine, the aim of smelting the steel with low contents of phosphorus, sulfur and hydrogen can be realized.