The compatibilizer with double comb structure has a superior compatibilizing effect for immiscible polymer blends due to the symmetrical structure on both sides of main chains. Extensive study related to the architectural effects of compatibilizer on the compatibilization has mainly focused on the side chains. We investigated the influence of the compatibilizer-main-chain structure on the compatibilizing effect for immiscible poly(vinylidene fluoride)/poly(L-lactic acid) (PVDF/PLLA) blends. Two reactive-comb compatibilizers with polystyrene (PS) and polymethylmethacrylate (PMMA) as main chains and PMMA as the side chains have been synthesized. PS is immiscible with both PLLA and PVDF, while PMMA is miscible with PVDF. It was found that both compatibilizers can improve the compatibility between the PLLA and PVDF, with different compatibilization effects. In the PVDF/PLLA (50/50) blends, 1 wt.% poly(styrene-co-glycidyl methacrylate)-graft-poly(methyl methacrylate) (RC–SG) tuned the morphology from the droplet-in-matrix structure to the co-continuous structure, while the blends with poly(methyl methacrylate-co-glycidyl methacrylate)-graft-poly(methyl methacrylate) (RC–MMG) kept the sea-island structure with even 3 wt.% loading. Moreover, RC–SG induces a wider co-continuous interval range than RC–MMG. The co-continuous structure obtained by RC–SG was also more stable than that by RC–MMG. It was further found that RC–SG-compatibilized PVDF/PLLA blends exhibit higher mechanical properties than the RC–MMG-compatibilized blends.