The inclusive $J/\Psi$ production by direct and resolved photoproduction in the $\gamma p$ scattering is calculated based on the nonrelativistic quantum chromodynamics (NRQCD) factorization formalism, which is in good agreement with the experimental data of total cross section distribution of heavy quarkonium production at HERA. Then we extend the formalism including the direct and resolved photoproduction processes to resolved pomeron model to study the heavy quarkonium photoproduction at the LHC energies. We present the predictions of rapidity and transverse momentum distributions of the inclusive diffractive $J/\Psi$, $\Psi(2S)$ and $\Upsilon$ photoproduction in $pp$, $pPb$ and $PbPb$ collisions at the LHC energies. Our numerical results indicate that the resolved photoproduction processes play an important role in the heavy quarkonium production. Especially for $pp$ collisions, the contribution of resolved photoproduction processes is the largest, which can reach to $28\%$, $13\%$ and $44\%$ for the rapidity distributions of $J/\Psi$, $\Psi(2S)$ and $\Upsilon$ inclusive diffractive photoproduction, respectively.