Magnolia lucida (Magnoliaceae) is classified as an endangered species by the International Union for Conservation of Nature. It has high commercial value owing to its attractive tree shape and flowers. We adopted an excellent genotype of M. lucida as the parent material and established a mini-cut orchard through grafting to provide trunk shoots explants over the long-term. Optimal sterilization was achieved using a combination of 75% ethanol for 30 s, one percent benzalkonium bromide for five minutes, and 0.1% mercuric chloride for five minutes. Modified Murashige and Skoog medium (ML) was the optimal medium for the growth of M. lucida. Addition of one mg/L of 6-benzyl adenine (BA) and 0.05 mg/L of α-naphthaleneacetic acid (NAA) to the medium increased the shoot induction rate to 95.56%, and the ML medium containing 0.4 mg/L BA and 0.04 mg/L NAA achieved the maximum multiplication rate (284.56%). Dark treatment for seven days, followed by continuous light treatment could better resolve the challenge of difficult rooting in M. lucida plants. Using random amplified polymorphic DNA and inter simple sequence repeat markers, we confirmed the genetic uniformity and stability of the regenerated plants. Our protocol should be helpful for the propagation and conservation of this endangered plant.