Polyoxometalate-based nanocomposites with electrocatalytic activity have been applied in hydrogen evolution reactions (HER). Seawater as the main water resource on the earth should be developed as the water electrolysis to prepare high-purity hydrogen. In this paper, we used two synthesis strategies to prepare the nanocomposite Co₄-POM@Co-PGDY (Co₄-POM: the Kegging-type microcrystals of K₁₀[Co₄(PW₉O₃₄)₂] and Co-PGDY: cobalt-porphyrin linked graphdiyne) with excellent activity for HER. Co-PGDY as the porous material is applied not only as the protection of microcrystals towards the metal ion in seawater but also as the co-electrocatalyst of Co₄-POM. Co₄-POM@Co-PGDY exhibits excellent HER performance in seawater electrolytes with low overpotential and high stability at high density. Moreover, we have observed a key H₃O⁺ intermediate emergence on the surface of nanocomposite during hydrogen evolution process in seawater by Raman synchrotron radiation-based Fourier transform infrared (SR-FTIR). The results in this paper provide an effective strategy for preparing polyoxometalate-based electrocatalysts with high-performance toward hydrogen evolution reaction.