We propose a nonlinear probabilistic generative model of Koopman mode decomposition based on an unsupervised gaussian process. Existing data-driven methods for Koopman mode decomposition have focused on estimating the quantities specified by Koopman mode decomposition: eigenvalues, eigenfunctions, and modes. Our model enables the simultaneous estimation of these quantities and latent variables governed by an unknown dynamical system. Furthermore, we introduce an efficient strategy to estimate the parameters of our model by low-rank approximations of covariance matrices. Applying the proposed model to both synthetic data and a real-world epidemiological data set, we show that various analyses are available using the estimated parameters.