The vortex pinning determining the current carrying capacity of a superconductor is an important property to the applications of superconducting materials. For layered superconductors, the vortex pinning can be enhanced by a strong interlayer interaction in accompany with a suppression of superconducting anisotropy, which remains to be investigated in iron based superconductors (FeSCs) with the layered structure. Here, based on the transport and magnetic torque measurements, we experimentally investigate the vortex pinning in two bilayer FeSCs, CaKFe₄As₄(Fe1144) and KCa₂Fe₄As₄F₂(Fe12442), and compare their superconducting anisotropy γ. While the anisotropy γ ≈ 3 for Fe1144 is much smaller than γ ≈ 15 in Fe12442 around T _c, a higher flux pinning energy as evidenced by a higher critical current density is found in Fe1144, as compared with the case of Fe12442. In combination with the literature data of Ba_0.72K_0.28Fe₂As₂ and NdFeAsO_0.82F_0.18, we reveal an anti-correlation between the pinning energy and the superconducting anisotropy in these FeSCs. Our results thus suggest that the interlayer interaction can not be neglected when considering the vortex pinning in FeSCs.