dispersive interaction together with a microwave drive applied to the qubit gives rise to a Kerr resonator with two-photon driving that enables us to efficiently engineer the quantum state of the resonator such as generation of the Schrodinger cat states for resonator-based universal quantum computation. Moreover, the presented architecture is easily scalable for solving optimization problem mapped into the Ising spin glass model, and thus served as a platform for quantum annealing. Although various scalable architecture with superconducting qubits have been proposed for realizing quantum annealer, the existing annealers are currently limited to the coherent time of the qubits. Here, based on the protocol for realizing two-photon driven Kerr resonator in three-dimensional circuit QED (3D cQED), we propose a flexible and scalable hardware for implementing quantum annealer that combines the advantage of the long coherence times attainable in 3D cQED and the recently proposed resonator based Lechner-Hauke-Zoller (LHZ) scheme. In the proposed resonator based LHZ annealer, each spin is encoded in the subspace formed by two coherent state of 3D microwave superconducting resonator with opposite phase, and thus the fully-connected Ising model is mapped onto the network of the resonator with local tunable three-resonator interaction. This hardware architecture provides a promising physical platform for realizing quantum annealer with improved coherence.