Interdisciplinary research collaboration is an important form and trend of academic research. It will have a profound impact on future scientific development and will play a significant role in promoting knowledge innovation and social progress. Exploring the operational mechanism of interdisciplinary research collaboration and clarifying its key elements and mechanism will help promote the efficient operation and sustainable development of collaboration. The article takes Stanford University's interdisciplinary research institutions as examples to analyze the key elements of interdisciplinary research collaboration practice from the perspective of organization, in views of the value perception and collaboration atmosphere, academic communication mode and scientific research infrastructure, team cohesion, interest protection mechanism, mission and objectives, policies and strategies, research funding, and management models. Based on case analysis, it builds an interdisciplinary research collaboration operation model from the perspective of organization, covering three layers of elements, namely "Three stages, one link, eight influencing factors".