Gallic acid (GA) is a naturally occurring polyphenolic compound exhibiting anti-tumor activity. To clarify the capability of GA in optimizing the in vitro/in vivo properties of the first line anti-tumor drug 5-fluorouracil (5-FU) and achieve synergistically enhanced anti-tumor activity, a novel cocrystal hydrate of 5-FU-GA-H2O was successfully screened and characterized based on various spectroscopic and experimental analysis including Fourier transform infrared spectroscopy (FT-IR), Raman spectra (Raman), powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric (TG) and scanning electric microscope (SEM) techniques. The results suggested the existence of hydrogen bonding interactions between C=O group of 5-FU and O–H group of GA. Although the dissolution rate and solubility of 5-FU-GA-H2O cocrystal were slowed and lowered compared with that of 5-FU, respectively, the membrane permeability was enhanced for cocrystal compared with that of intact 5-FU and physical mixture (PM) of 5-FU and GA. For the cocrystal, the cumulative amount per unit area of permeated 5-FU in the first 10 h was 2.56 and 9.97 times of that of pure 5-FU and PM, respectively, in the case that transmembrane behavior of 5-FU depended on the type of solution from which the powder was dissolved. Meanwhile, improvement on oral bioavailability by co-crystallization was observed; AUC0-t of cocrystal was 2.78-fold higher than that of 5-FU. Furthermore, the cocrystal displayed a superior cytotoxic activity on 4T1 mouse breast cancer cells compared with pure 5-FU and even the PM. It was confirmed that the cocrystal solution induced higher autophagic flux than those of 5-FU and PM in 4T1 cell, suggesting that autophagy rather than apoptosis mainly mediated cell death. The obvious difference of tumor inhibition activity between PM and cocrystal in intraperitoneal injection administration indicated that some of the interactions formed in the solid cocrystal could retain in solution in some way. Benefiting from synergistic cytotoxicity, drug efficacy in vivo was enhanced through injection administration of solution from which cocrystal was dissolved.