Due to extensive introduction and breeding, the taxonomic relationships of Lonicera L. are unclear. Alternative scientific methods are needed to explore the classification of these new Lonicera. In this paper, the pollen morphology characteristics, karyotype features, and floral and fruit pigment components of 13 taxa of Lonicera were analyzed by means of scanning electron microscopy, karyotype analysis, High Performance Liquid Chromatography Mass Spectrometry (HPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The 13 representatives of Lonicera were divided into groups of four, three, three and three taxa through the analysis of pollen morphology characteristics, karyotype features, floral composition and fruit pigment composition, respectively. Lonicera ruprechtiana and Lonicera tatarica always clustered together. Five hybrids, including Lonicera korolkow × Lonicera maackii and Lonicera korolkow × Lonicera tatarica No. 8 can generally be clustered with their parents. These results indicate that the analysis of pollen morphology characteristics, karyotype features, and floral and fruit pigment composition has value and significance for the study of systematic classification and relationships, and the conclusions of this study partially support morphological taxonomy.