The Jasa Webometrics Indonesia Ranking methodology is based on four indicators, namely presence, visibility, transparency, and excellence. These indicators are used to measure the web presence and online impact of universities and research institutions.

Presence measures the size of a university's web presence, including the number of web pages, subdomains, and rich files. Visibility measures the level of external impact of a university's web presence, including the number of backlinks from other websites. Transparency measures the level of open access and dissemination of a university's research output, including the number of files in academic repositories. Excellence measures the level of academic and research performance of a university based on the number of citations received.

The Webometrics Ranking methodology is unique in that it considers both the size and quality of a university's web presence. It also takes into account the open access and dissemination of a university's research output, which is becoming increasingly important in today's research environment.