In this study, the compressive strength of an ancient masonry structure was investigated. Taking the first story of a pagoda as the prototype structure, three model specimens were generated by old bricks in different scales: the original brick scaled to 1, the model brick scaled to 1/4, and the model brick scaled to 1/8. The compression tests were then carried out. The characteristics of the structural cracks developed during the loading process were observed. And the numerical simulation was carried out, the structural load, displacements, and strains were determined, and the stresses and failure modes of the three models were compared. Furthermore, the compression failure mechanisms and damage variation characteristics of the models were analyzed. The results indicate that the failure process of masonry pagodas under compression occurs in three stages, which are the initial cracking along the mortar joint, the expansion and extension of the cracks, and the running through of the cracks. The cracking of pagodas starts at the top four corners, gradually extends downwards, and finally runs through the entire structure with the increase in loading. Small section brick columns were informed, leading to structural failure owing to instability. In addition, horizontal deformation occurred along both inside and outside of the pagoda wall, and some bricks were cracked. The initial damage and stiffness of the model structure varied due to the different sizes of bricks. The cracking load and ultimate strength decreased with unit block size decreasing, while the strain followed an inverse trend. Based on the total and partial deformation characteristics of the model pagoda structure, the failure mechanism of the ancient pagoda under compression was analyzed, and the damage evolution parameter was calculated. The findings of this study provide valuable references for the safety assessment of ancient masonry pagodas.