The invention provides a method for extracting and separating silkworm pupa protein from silkworm pupas through ionic liquid. The raw materials comprise fresh pupas, dried pupas and degreased dried pupas. The method comprises the steps that the ionic liquid is used as a solvent to dissolve silkworm pupa powder on the condition of heating and stirring, the mass ratio of the raw materials to the ionic liquid is 1:1-1:50, the heating temperature is 0-130 DEG C, the heating time is 1-96 h, and centrifugation is carried out when the product is hot. The ionic liquid in the obtained silkworm pupa protein and ionic liquid mixed solution is eluted through a regeneration precipitator, and therefore the regeneration silkworm pupa protein is obtained. According to the method, the ionic liquid is adopted as the solvent, operation is easy and free of pollution, corrosion of a traditional alkali-solution and acid-isolation method to equipment is avoided, and the fat content in the obtained silkworm pupa protein is low. The raw materials are low in cost and easy to obtain, and the new method is provided for efficient utilization of resources.