Gaussian process state-space models (GPSSMs) offer a principled framework for learning and inference in nonlinear dynamical systems with uncertainty quantification. However, existing GPSSMs are limited by the use of multiple independent stationary Gaussian processes (GPs), leading to prohibitive computational and parametric complexity in high-dimensional settings and restricted modeling capacity for non-stationary dynamics. To address these challenges, we propose an efficient transformed Gaussian process state-space model (ETGPSSM) for scalable and flexible modeling of high-dimensional, non-stationary dynamical systems. Specifically, our ETGPSSM integrates a single shared GP with input-dependent normalizing flows, yielding an expressive non-stationary implicit process prior that can capture complex transition dynamics while significantly reducing model complexity. For the inference of the implicit process, we develop a variational inference algorithm that jointly approximates the posterior over the underlying GP and the neural network parameters defining the normalizing flows. To avoid explicit variational parameterization of the latent states, we further incorporate the ensemble Kalman filter (EnKF) into the variational framework, enabling accurate and efficient state estimation. Extensive empirical evaluations on synthetic and real-world datasets demonstrate the superior performance of our ETGPSSM in system dynamics learning, high-dimensional state estimation, and time-series forecasting, outperforming existing GPSSMs and neural network-based SSMs in terms of computational efficiency and accuracy.