Current quantum computers are limited in the number of qubits and coherence time, constraining the algorithms executable with sufficient fidelity. Variational quantum eigensolver (VQE) is an algorithm to find an approximate ground state of a quantum system and expected to work on even such a device. The deep VQE [K. Fujii, et al., arXiv:2007.10917] is an extension of the original VQE algorithm, which takes a divide-and-conquer approach to relax the hardware requirement. While the deep VQE is successfully applied for spin models and periodic material, its validity on a molecule, where the Hamiltonian is highly non-local in the qubit basis, is still unexplored. Here, we discuss the performance of the deep VQE algorithm applied to quantum chemistry problems. Specifically, we examine different subspace forming methods and compare their accuracy and complexity on a ten H-atom tree-like molecule as well as a 13 H-atom version. Additionally, we propose multiple methods to lower the number of qubits required to calculate the ground state of a molecule. We find that the deep VQE can simulate the electron-correlation energy of the ground-state to an error of below 1%, thus helping us to reach chemical accuracy in some cases. The accuracy differences and qubits reduction highlights the basis creation method's impact on the deep VQE.