The paper adopts a historical analysis method. By analyzing the transformation of the main research objects, organizational structure and the kinds of scientific research institutions of scientific organization paradigm in each period, we finally sort out the transformation of the scientific organization paradigm, and deeply analyze the historical evolution of scientific research institutions. Based on the development tendency of data-driven science, collaborative science, open science and citizen science, the author believes that scientific research institutions are developing to data-intensive scientific paradigm, and the management paradigm shows more characteristics of cross-institution, inter-discipline, openness and clear responsibility. In the future, the public need to take part in scientific research activities with the guidance of an open-participation scientific research organization paradigm, thus promoting the scientific research industry to move forward.