We have investigated the vortices pinning behaviors of CaKFe4As4 with two types of defect structures by alternating current and direct current susceptibility measurements under the Ginzburg-Landau theory and collective pinning model. We observed a new dissipative peak at temperature T
J in each out-of-phase () curve even at low magnetic field in the samples with thick CaFe2As2 intercalations, which has been ascribed to the weak Josephson-like link. The unrelaxed current J
c and the normalized pinning energy g(t) have been investigated for both types of the CaKFe4As4 crystals based on the dynamic relaxation rate Q and transient current J
s by means of generalized inversion scheme. For the samples with monolayer-KFe2As2 intercalations, the temperature dependence of J
c and g(t) is found to be in agreement well with the model of single vortex δT
c-pinning. But for the samples with thick CaFe2As2 intergrowths, both the δT
c- and δl-pinning are in functioning at low magnetic field, but the δl pinning will play a leading role at magnetic field above 3.0 T. Differential charge analysis shows that the intergrowth of KFe2As2 should be normal phase and the CaFe2As2 will become superconducting one due to the charge transfer. The non-superconducting KFe2As2 will induce an abruptly spatial change of T
c resulting to strong δT
c-pinning, and the superconducting CaFe2As2 phase can mainly cause to fluctuate of mean free path leading to δl-pinning. The present work illustrates how the defect structure affects the flux pinning behaviors and can provide a new clue to design high-performance superconducting wire/tapes and films for strong magnetic field applications.