Spin-orbit coupling (SOC) has long been regarded as the core interaction to determine the efficiency of spin conserved transport in semiconductor spintronics. In this report, a spin-valve device with a Co/metal-free phthalocyanine (H2Pc)/Co stacking structure is fabricated. The magnetoresistance effect was successfully obtained in the device. It is also found that the magnetoresistance response is relatively smaller than that of metallic phthalocyanines, clearly implying that SOC is not the key factor to affect the magnetoresistance in phthalocyanine spin-valves. The dominant mechanism that determines the spin transport efficiency in the present H2Pc devices was systemically explored by combining both experimental measurements and first-principles calculation analysis. It was noticed that both the crystalline structure and molecular orientation of the H2Pc layer could be modified by the contact under-layer materials, which changes the magnetization intensity of the ferromagnetic metallic electrode due to the strong interface hybridization of Co/H2Pc. Meanwhile, the theoretical calculations clearly demonstrated that the spin filter effect from the second H2Pc layer should be responsible for the decrease of the magnetoresistance response in the present spin-valves compared to those using metallic phthalocyanine layers. This investigation may trigger new insights into the role of SOC strength and interface hybridization in organic spintronics.