Daidzein (DAI) and betaine (BTN) exhibit outstanding therapeutic effects on the treatment of obesity and lipid-related diseases. However, the low solubility and oral bioavailability of DAI, along with the poor stability of BTN, limit the clinical application of both compounds. Here, a novel 1:2 drug-drug cocrystal of daidzein and betaine (DAI-BTN) was successfully prepared using crystal engineering technology. Dynamic vapor sorption analysis showed that the mass change of DAI-BTN was reduced by 58 % in a relatively humidity range of 0 %–95 % compared to BTN. As compared to pure DAI, the intrinsic dissolution rate and the bioavailability of DAI-BTN were enhanced by 4.34-fold and 3.73-fold, respectively. Furthermore, the effect and mechanisms of DAI-BTN in a mouse model of diet-induced obesity were explored. The results showed that the DAI-BTN can reduce body weight and adipocyte area, which were negatively correlated with the levels of TG, TC, LDL-C, AST, ALT, TNF-α, IL-1β and IL-6. Particularly, DAI-BTN was associated with improving the diversity, structure, and composition of the gut microbiome, promoted the growth of beneficial bacteria (e.g., Proteobacteria and Akkermansia) and inhibited the proliferation of harmful bacteria (e.g., Desulfovibrio and Flexispira). Therefore, DAI-BTN hold great promise to be developed as an effective drug combination agent for the alleviation of obesity.