The invention belongs to the field of chemistry and chemical engineering, and particularly discloses a catalyst for selectively hydrogenating dimethyl terephthalate to prepare 1,4-cyclohexane dimethyl isophthalate and a preparation method and use method of the catalyst. The catalyst is Ru particles, and the surfaces of the Ru particles are modified with Ru-S and Ru-O coordinate bonds. The preparation method comprises the steps of solution preparation, a reduction reaction, sedimentation and washing, molecular modification and aftertreatment. Compared with the prior art, the catalyst is used for selectively hydrogenating dimethyl terephthalate to prepare 1,4-cyclohexane dimethyl isophthalate, better catalytic activity and target product selectivity are achieved, hydrogenation conditions are mild, and reaction time is shorter.