The properties of storage system structures were largely determined by the particle size and compressive modulus of the granular material inside, which is an important issue for silo structure design. The large compressibility and complex contact relationship of granular materials in the cell are needed for the reliable pressure measurement. A set of testing system and experiment method were designed to reveal the size effect of earth pressure cells in the loading and unloading process of granular materials. Different compressive moduli were adopted for the selection of the appropriate granular particle size. Four types of granular materials including fine sand, coarse sand, rapeseed, and wheat were used as raw materials. Three types of earth pressure cells were used in this study with different sizes, and a series of loading and unloading tests were conducted with liquid. The interaction between the cell and granular material and its main factors were discussed. The results show that the pressure exhibits a linear relationship with the strain in the loading and unloading process in liquid surroundings. Owing to the interaction between the cell and granular materials, the pressure increased linearly with the strain in the loading process as well as a nonlinear relationship were exhibited in the unloading process. In the unloading process, an exponential model was proposed to simulate the pressure and strain based on the significant hysteresis phenomenon observed during unloading process. The hysteresis ratio (R) index was adopted to evaluate the hysteresis. It was found that the material type of surroundings and particle size were believed to be the two major factors affecting the R value. To improve the accuracy of granular material interface pressure measurement, the earth pressure cell with a d/d0 ratio exceeding 11 was recommended. The results obtained in this study provide theoretical foundation for energy saving and safety granary structure design.