An innovative method using a methanol solution of barium hydroxide-urea as a protective agent was investigated for the conservation of stone artifacts with harmful gypsum weathering crusts. In this method, the methanol solution of barium hydroxide-urea and water were introduced into the gypsum crust in sequence by surface spraying. By doing so, the harmful gypsum crust is directly converted into a barium sulfate—calcium carbonate composite protective layer. The properties of the composite layer were characterized by SEM-EDX, XRD, ATR-FTIR, IC, water solubility, wetting angle, color difference, open porosity, capillary water absorption, and surface hardness. The results of the morphological and composition characterization (SEM-EDX, XRD, ATR-FTIR) indicate that the added urea can promote the carbonization reaction effectively. In addition, the methanol solution of barium hydroxide-urea can penetrate deep into the gypsum crust. The results of the physical properties characterization denote that the water stability of the specimens was significantly increased after the protection treatment; an approximate ten-fold stronger water resistance ability was achieved. Meanwhile, the intrinsic physical properties of gypsum crust, such as pore structure and original appearance, could basically be maintained. The presented conservative method has high facility and controllability and satisfying conservation effect, which means it has potential in the conservation of surface weathering carbonate stone artifacts.