The bark of Magnolia officinalis is a well-known Traditional Chinese Medicine. In the present study, two new alkaloids, named (S)-4-keto-magnoflorine (6) and (R)-3,4-dehydromagnocurarine (11), together with seven known alkaloids: (S)-magnoflorine (5), trans/cisN-feruloylputrescine (7/8), (R)-magnocurarine (10), (S)-tembetarine (12), (R)-oblongine (14), and (R)-asimilobine (17) were isolated and their structures elucidated by spectroscopic methods, including 1D, 2D NMR, and HRESI-MS. The absolute configurations of the isoquinoline alkaloids 5, 6, 10–12, 14, and 17 were determined by CD. In vitro inhibitory activities against aldose reductase, lipase, α-glucosidase, DPP–IV and three cancer cell lines (A549, Bel-7402, and HCT-8) were evaluated for all isolated compounds. However, all compounds showed weak activities in all tests at the same concentration as the positive control drugs. An HPLC-ESI-MSn method has been established for screening of alkaloids in the bark of M. officinalis. A total of 23 alkaloids were identified or tentatively characterized; including 13 aporphines, eight benzylisoquinolines and two amides. Plausible fragmentation pathways of the representative compounds 6, 7/8, 11, and 17 were proposed in the present study.