Blue honeysuckle (Lonicera caerulea L.), which belongs to the Caprifoliaceae family, is an emerging fruit crop worldwide. For the development of a transgenic system and multipurpose tissue culture, this study for the first time established an in vitro regeneration system via somatic embryogenesis, as well as improving the previously established indirect organogenesis-based regeneration system. For embryogenesis, Murashige and Skoog (MS) medium supplemented with 1.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) showed the highest induction rate of the embryogenic callus (97.6%), and MS supplemented with 0.1 mg/L 6-benzyladenine (6-BA), 0.1 mg/L α-naphthaleneacetic acid (NAA), and 0.5 g/L activated carbon (AC) achieved the highest somatic embryo rate (28.3%). For indirect organogenesis, MS medium supplemented with 1.0 mg/L 6-BA and 0.1 mg/L NAA resulted in the highest non-embryogenic callus induction rate (98.9%) and adventitious shoot induction rate (51.6%). For adventitious root induction, MS supplemented with 1.0 mg/L indole-3-butyric acid (IBA) achieved the highest root induction rate (96.0%) and average root length (4.6 cm), whereas MS supplemented with 0.5 mg/L indole-3-acetic acid (IAA) resulted in the highest average regenerated root number (8.8). The total time for the regeneration from explants to soil-planted seedlings (10 euphylla) was 105 and 150 days with an efficiency of 44.1% and 23.9% through organogenesis and somatic embryogenesis, respectively. This study provides a powerful tool for rapid propagation, proliferation, and transformation, as well as laying a technological foundation for gene function research and genetic improvement of blue honeysuckle.