The invention belongs to the field of road engineering materials, and particularly relates to a composite water permeable brick and a preparation method thereof. The provided water permeable brick comprises a concrete slab body layer, a bonding layer and a flexible wearing layer which are in contact successively, the flexible wearing layer is prepared from an organic cementing material and a grading gravel mixed material, the organic cementing material is prepared from modified bitumen and / or a modified polymer, and the grading gravel mixed material is prepared from the following components inparts by weight: 12-26 parts of 1-3 mm of gravels, 35-90 parts of 3-5 mm of gravels, 0-30 parts of 5-10 mm of gravels, 0-20 parts of 10-16 mm of gravels, 0-3 parts of cement, and 0-4 parts of a pigment. The provided composite water permeable brick is formed by the rigid concrete layer and the flexible wearing layer, and has the advantages of water permeability, wear resistance, skid resistance, high strength and the like, these advantages can solve quality problems of freeze-thaw damage, peeling, corroding, swelling, soaking corrosion by rainwater and snowmelt and the like of an existing pavement brick; the service life of the pavement brick is prolonged.