As a valid tool for solving ground state problems, imaginary time evolution (ITE) is widely used in physical and chemical simulations. Different ITE-based algorithms in their quantum counterpart have recently been proposed and applied to some real systems. We experimentally realize the variational-based quantum imaginary time evolution (QITE) algorithm to simulate the ground state energy of hydrogen (H2) and lithium hydride (LiH) molecules in a superconducting qubit system. The H2 molecule is directly simulated using the 3-qubit circuit with unitary-coupled clusters (UCC) ansatz. We also combine QITE with the cluster mean-field (CMF) method to obtain an effective Hamiltonian. The LiH molecule is correspondingly simulated using the 3-qubit circuit with hardware-efficient ansatz. For comparison, the LiH molecule is also directly simulated using the 4-qubit circuit with UCC ansatz at the equilibrium point. All the experimental results show a convergence within 4 iterations, with high-fidelity ground state energy obtained. For a more complex system in the future, the CMF may allow further grouping of interactions to obtain an effective Hamiltonian, then the hybrid QITE algorithm can possibly simulate a relatively large-scale system with fewer qubits.