In order to efficiently use Malus baccata(L.) Borkh germplasm, this study analyzed the phenotypic diversity of 19 morphological traits such as leaf shape, fruit shape and tree performance of 239 Malus baccata (L.) Borkh germplasm which collected in northern China. The results showed that Malus baccata (L.) Borkh in Heilongjiang province and Nei Monggol Autonomous Region were rich in phenotypic diversity, with mean variation coefficient(VC) of 32.65% and Shannon’s diversity index( H') of 1.38. The CV and H' for 13 qualitative characters of Malus baccata (L.) Borkh such as tree performance and tree shape were 38.43% and 0.95, while were 26.87% and 1.80 for 6 quantitative characters such as leaf length and lead width. Further analysis showed that phenotypic diversity of Malus baccata (L.) Borkh exist differences among different regions, which was the highest in Wenchun of Heilongjiang. Cluster analysis based on 19 morphological traits showed that all of materials could be divided into 2 populations, 7 subpopulations and 12 inferior subpopulations when the euclidean distance in 2.5. It implied that there had been complex genetic basis for Malus baccata (L.) Borkh because of all of materials were dispersed and did not form a separate population.