The invention discloses a special complex enzyme system for kelp comprehensive utilization and application thereof. The complex enzyme system comprises an enzyme A and an enzyme B, wherein the enzyme A comprises any four or more than four kinds of materials from cellulose, hemicellulase, pectinase, amylase, xylanase, alkaline cellulose, pentosanase, glucanase and feruloyl esterase; the enzyme B comprises one or any two kinds of materials from alkaline protease, neutral protease, papain, trypsin, acid proteinase and pepsin. The complex enzyme system has the prominent beneficial effects that after the complex enzyme system is used, four kinds of products of fucoidin, alginic acid, mannitol and functional dietary fiber can be simultaneously extracted from kelps; the extraction ratio of four kinds of active ingredients reaches more than 90 percent (through being metered by the kelp dry weight); the comprehensive utilization rate of kelp resources is obviously improved; the product additional values of kelp processing industry are greatly increased; the technological level of relative products is improved.