China is one of the most important fruit tree origin centers in the world, and in the evolution of deciduous fruit tree farmers, the kinship background of fruit trees has a certain probability of heterozygosity, resulting in some difficulties in classification and utilization. In addition, many farm varieties have the same name but foreign bodies, and it is not possible to judge their classification system by name. Pollen characteristics are controlled by genes and rarely change under the influence of the external environment, which can be used for identification and classification between plant species and even between varieties. In genetics, pollen shows strong conservation and stability, which indicates that plant pollen morphology is helpful for the classification and identification of plant species and varieties, and is also of great significance in exploring the origin and evolution of plants. This dataset is a pollen scanning electron microscope observation of some excellent varieties of 11 tree species such as pomegranate, apple, peach, chestnut, walnut and grape in Liaoning, Shandong, Shaanxi and other key distribution areas and advantageous production areas in China from 2012 to 2017, and the data include: collection number, variety name, observation method, observation instrument and observation result information. The dataset has a total of 571 symbol records, and the article dataset is all raw data without any processing. In this study, scanning electron microscope was used to scan the pollen of some agricultural varieties of deciduous fruit trees in China's dominant production areas from 2012 to 2017, and the results of electron microscope observation and analysis were basically consistent with traditional taxonomy. Therefore,the results of electron pollen microscope analysis of farm varieties can be used for the identification and classification of farm varieties, and the differences in pollen morphology, size and outer wall ornament can provide a basis for the kinship and classification identification of farm varieties from the perspective of spores.