The Great Wall is a world cultural heritage, and mortar is the key material in its conservation and restoration. In this study, the composition, crystal structure and microscopic morphology of the Great Wall masonry mortar in Yanqing and Huairou areas and the mortar in different parts of the Great Wall of Yanqing were systematically analyzed by microscopic analysis and testing methods such as X-ray fluorescence spectroscopy, X-ray diffractometry, thermogravimetric analysis, scanning electron microscopy and Fourier infrared spectroscopy. The results show that the composition of the Great Wall masonry mortar in Yanqing and Huairou areas is quite different. The content of Mg, Si and organic matter in Huairou mortar is much higher than that in Yanqing mortar. This is because Huairou mortar stone material may contain more magnesite, and Huairou mortar contains a small amount of sand. The masonry mortars in both areas contain glutinous rice, which results in a smaller crystal grain size of CaCO3 and a denser structure. There are also differences in the composition of mortar for different parts in the same area. The grouting mortar is quite different from other types of mortar, and contains more sand and stone. And the stone joint mortar contains a small amount of fine sand. The pavement masonry mortar is not fully carbonized, and contains a small amount of Mg(OH)2 and Ca(OH)2. The presence of glutinous rice is detected in brick masonry, jointing, and pavement masonry mortar, but no glutinous rice is detected in grouting and stone joint mortar. This study will provide a theoretical basis for the formulation of the Great Wall repair mortar.