Quantum neural networks are promising for a wide range of applications in the Noisy Intermediate-Scale Quantum era. As such, there is an increasing demand for automatic quantum neural architecture search. We tackle this challenge by designing a quantum circuits metric for Bayesian optimization with Gaussian process. To this goal, we develop quantum gates distance that characterizes the gates' action over every quantum state and provide a theoretical perspective on its geometric properties. Our approach significantly outperforms the benchmark on three empirical quantum machine learning problems including training a quantum generative adversarial network, solving combinatorial optimization in the MaxCut problem, and simulating quantum Fourier transform. Our method can be extended to characterize behaviors of various quantum machine learning models.