The school emblem is a circular pattern. The upper part of the school emblem surrounds the full name of the Chinese school name standard from left to right, the lower part surrounds the full name of the English school name standard from left to right, and the middle is a begonia-style hole and window pattern. The cave window design is based on the landmark building "Big Bell Tower" of National Guangdong University. By using the artistic conception and modern design techniques of China Garden, the begonia-style cave window is combined with the appearance of the big bell tower in the garden to form the word "Zhongshan". The trees on both sides of the cave window form a far-reaching space from big to small, which enhances the layering and three-dimensional sense. The arc in the middle skillfully forms a red cotton, which is a symbolic tree species in Lingnan area, implying that Sun Yat-sen University is rooted in Lingnan area. The profound road formed by a school year "1924" embodies the profound academic accumulation and brilliant historical process of Sun Yat-sen University.

The emblem of Sun Yat-sen University is usually standard green, representing life, development and eternity, and symbolizing the vitality and vigor of Sun Yat-sen University.