The compound enzymatic hydrolysate of Porphyra (CPEH) was prepared using a novel porphyranase (EC 3.2.1.178) and neutral protease. Then 16S rRNA gene sequencing, gas chromatography and real-time PCR analysis were used to analyze the effects of CPEH on diet-induced obesity (DIO) and gut microbiome in HFD-fed mice. The results suggested that CPEH improved blood lipid levels, alleviated body fat deposition, and reduced adipocyte size. Possibly because CPEH could repress the expression of genes (DGAT1 and DGAT2) related to triglyceride synthesis in liver, and promote gene expression of enzymes (ATGL and HSL) related to lipolysis in adipose tissue. Furthermore, CPEH promoted the proliferation of beneficial bacteria (Muribaculaceae and Helicobacteraceae) related to obesity and repressed the growth of harmful bacteria (Streptococcaceae). CPEH also regulated the abundance of KEGG pathways associated with lipid metabolism, such as 'Glycerolipid_metabolism'. In summary, CPEH effectively prevented high fat diet-induced obesity and regulated gut microbial composition and function. CPEH has potential to be applied to the development of functional beverage. This study could contribute to the high value application of low valued Porphyra.