The dependence of optical clearing on properties of the different tissue structures is investigated in order to better know the clearing mechanisms and effective clearing approach. Two typical tissues, muscle and epithelial, have been chosen as the targets and the effect of optical clearing has been comparatively studied by optical coherence tomography (OCT) and near infrared spectroscopy (NIR) with the clearing agent glycerol used. The results show that the improved imaging depth and contrast among different layers in the porcine skeletal muscle and stomach mucosa are visualised with the OCT assessment. The overall increases in light transmittance in the muscle tissue and the stomach mucosal tissue after 30 min treatment are observed to be approximate 21% and 16%, decreases in diffuse reflectance are 33% and 21%, respectively, with the quantitative measurement of NIR. The clearing progress of each tissue type as a function of time corresponds very well with the respective loss in water dynamics shown by the near infrared spectra: early rapid transport, mid-linear and slow exponential diffusion for muscle tissue, and contrarily for stomach mucosa with an early very slow transport and later linear increasing efflux. The different permeabilities of muscle tissue and mucosal tissue are thought to be accountable for the difference in clearing effect between the two tissues. These observations confirm expectation that optical clearing is dependent on tissue structure in an explainable manner.