The methodology section of an article usually outlines the reasons the researchers chose the research method they did, which can include the principles of the method and the theory behind it. A method section would describe the process of collecting the data (e.g. recruitment, populations, documentation). In short, the methodology section usually describes the "why" of the research method, whereas the methods section describes the "how". This can be confusing as sometimes the terms are used interchangeably (Campbell, 2016).
Campbell, S. (2016). Perspectives: Method and methodology in nursing research. Journal of Research in Nursing, 21(8), 656-659. doi:10.1177/1744987116679583
