Square rebars were developed and used for decades in the early development of reinforced concrete (RC) structures; however, the objectives of modern concrete structure durability analyses and standards are centered on round rebars in past decades, which are not suited for RC buildings utilizing square rebars. Considering the absence of proper evaluation techniques to evaluate the square rebar RC structures’ durability accurately, a novel durability prediction method has been proposed for this type of historical building. The method is based on major parts as in-situ investigation, finite element model simulation, component importance analysis, and structural durability prediction. The durability prediction calculation method was established on the experimental results of the realistic historical concrete tests and corrosion-induced cover cracking experiments for square rebar components. It was found that the carbonization-resistant ability of historical concretes was relatively weaker than that of current concretes and the calculation method for critical corrosion depth of square rebar was different from that of round rebar. Furthermore, two typical application cases are presented to introduce the procedure of the method in detail. Consequently, the research outcomes can be directly used on the durability prediction and protection works for historical RC buildings.