The local investigations with citizen participation conducted by regional museums after 1970s in Japan provide a new pattern for how participatory approaches could be adopted by museums in the process of knowledge production. This pattern has two important features: one is a team work by the experts (the curators) and non-experts (the citizen) to build up the science knowledge about the locality in partnership. And more importantly, this pattern is a new museography developed under the influence of the governance of regional museums in Japan. The theory on regional museums in Japan was mainly developed from the perspective of social education, emphasizing that the public value of the regional museums is to produce and accumulate the knowledge of locality, and ensure the learning right of all the citizen. Furthermore, the regional museums should build up a partnership with citizen and play the role as facilitators to support citizen participation of local public issues. This paper reviews discussions of regional museums after 1950s, and their influence on the governance of the regional museums. The different practice of the local investigations with citizen participation is also discussed. Jannifer Barrett’s argument on the intellectual function of the museums and the role of the museums as pubic intellectuals is applied to exam meanings of this museum practice in Japan.