The invention discloses a thorium and uranium separating and recovering method. The method comprises the following steps: 1) taking aqueous acid containing thorium and uranium as material liquid, taking an organic solvent containing methylphosphonic acid di(1-methyl) heptyl ester, taking the aqueous acid as washing liquid for fractionation and extraction; 2) taking the organic solvent containing methylphosphonic acid di(1-methyl) heptyl ester as an extraction supplement agent, taking the aqueous acid as the washing liquid, and performing fractionation and extraction on an organic extract phase containing thorium and uranium, the extraction supplement agent, and the washing liquid; and 3) performing back extraction on the organic extract phase containing uranium and strip liquor in a multistage counter current mode. Under conditions of low feeding acidity, organic phase/water phase flow ratio and less extracting stage number, separating and recovery of thorium and uranium are realized, high thorium and uranium recovery rate can be obtained, and the impurity metal ion decontamination coefficient is obtained.