Growing attentions have been focused on natural antitumor drugs. Recently, a novel and potent antitumor drug Cheliensisin A (GC-51) with broad-spectrum efficiency has been developed. However, due to its poor water solubility and chemical instability, choosing the appropriate dosage form is of great significance. This study aimed at developing a lyophilized submicron emulsion for GC-51 and further improving the therapeutic index of the drug. The resultant lyophilized GC-51 submicron emulsion was much more stable than its solution, which can be stored for years without significant change on physicochemical properties. And its solubility was increased from 6.74 ± 0.14 to 2.00 ± 0.10 mg mL−1. The 50% inhibitory concentration IC50 values were calculated from growth curves by MTT assay on various tumor cell lines. Compared with the IC50 of GC-51 crude drug, that of lyophilized GC-51 submicron emulsion decreased from 24.04 ± 1.97 to 8.23 ± 1.84 μg mL−1 on HepG2, and from 31.08 ± 2.56 to 10.85 ± 2.09 μg mL−1 on CT-26, from 17.90 ± 1.83 to 7.49 ± 1.87 μg mL−1 on HeLa and from 16.38 ± 2.41 to 10.13 ± 2.12 μg mL−1 on A549, respectively. In the time-dependent assay of tumor cell viability, lyophilized GC-51 submicron emulsion exhibited significantly lower inhibition rate in the initial action times, but increased gradually afterwards. That means lyophilized submicron emulsion as the vector for GC-51 had some protective and delayed release effect. Further, the in vivo therapeutic efficacy was measured in pulmonary metastasis of colon cancer-bearing BALB/c mice model. An obvious enhanced antitumor activity was observed after administration of lyophilized GC-51 submicron emulsion (P < 0.05), which increased from 22.78 ± 3.5 to 41.42 ± 4.2% compared with GC-51 injection. And the life span of tumor-bearing mice in lyophilized GC-51 submicron emulsion group was significantly longer than that of the mice in GC-51 injection and normal saline groups. Compared with crude drug, the lyophilized GC-51 submicron emulsion showed a significantly higher antitumor efficiency both in vivo and in vitro, suggesting a potential application in tumor chemotherapy.