Three distinct systems of asphalt-based waterproof material structures were designed for building cement substrates. These asphalt-based waterproof materials were modified using either Styrene Butadiene Rubber (SBR) or Ethylene Acrylic Acid Copolymer (EAA) along with various inorganic fillers. To enhance the adhesion between the waterproof materials and the cement substrate, the surface of the cement substrate was chemically treated with either γ-methacryloyloxypropyltrimethoxy silane (KH-570) or vinyltrimethoxy silane (SG-Si 171) through atomization spraying and infrared irradiation. The adhesion properties and debonding failure modes of waterproof materials for cement substrates were analyzed, and six groups of samples with relatively good adhesion properties were screened for further environmental aging tests. The samples were subjected to temperature fluctuations, water immersion, freeze-thaw cycles, thermal aging, acid, alkali, and salt, to identify favorable asphalt-based waterproof structure systems for five climate zones, acid rain-affected regions, and saline-alkali-affected regions in China. These results provide valuable insights for designing effective waterproof materials for different environments.