The invention relates to the field of water leakage treatment of building joints, in particular to a deformation joint treatment method and a deformation joint waterproof structure. The deformation joint treatment method comprises the steps that 1, on-site survey is conducted; 2, the type of deformation joint leakage is determined based on the result of the on-site survey; and 3, a construction plan is made based on the type of the deformation joint leakage. According to the deformation joint treatment method, the on-site survey is firstly conducted, information of the deformation joint is collected, the width and length of the deformation joint, the location and cause of water seepage, the number of water seepage points, the amount of water seepage, and the damage condition of a water stop are obtained; the type of the deformation joint leakage is determined based on the location and cause of water seepage, the number of water seepage, the amount of water seepage, and the damage condition of the water stop; according to the determined type of the deformation joint leakage, a targeted construction plan is made to better treat the leakage. According to the deformation joint treatment method, a flexible waterproof structure is formed, in the process of water blocking, a water blocking material can passively adapt to the deformation of the structure, and the problem of water leakage caused by the material damage due to the deformation of the structure is alleviated.