Study on the microscopic structure of clathrate hydrate has made significant progress in the past decades. This review aims to summarize the state of the art of the experimental characterization of guest molecular occupancy in clathrate hydrate cages, which is an important area of the microscopic structures. The characterizing method and features of different guest molecular, such as hydrocarbon, carbon dioxide, hydrogen and inhibitor/ promoter, in different hydrate cages have been extensively reviewed. A comprehensive use of advanced technologies such as X-ray diffraction, Raman spectroscopy and nuclear magnetic resonance may provide better understanding on the compositions and microscopic mechanisms of clathrate hydrate. (C) 2019 The Chemical industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights reserved.