Abstract: Methodology is one of the core issues in the research on contemporary science-religion relation. Particularly speaking, Barbour's biggest contribution is to involve the methodology of critical realism into the field of traditional science-religion relation. Actually,Barbour's fourfold typology is based on this methodology which refers to analogy and mode research. The common point for analogy is that science and religion can be both regarded as social institution. What Barbour did on critical realism is to inherit its reasonable methodology and carry out ontological reconstruction with the aid of process thought.