Partial differential equations (PDEs) are widely used for description of physical and engineering phenomena. Some key parameters involved in PDEs, which represents certain physical properties with important scientific interpretations, are difficult or even impossible to be measured directly. Estimation of these parameters from noisy and sparse experimental data of related physical quantities is an important task. Many methods for PDE parameter inference involve a large number of evaluations of numerical solution of PDE through algorithms such as finite element method, which can be time-consuming especially for nonlinear PDEs. In this paper, we propose a novel method for estimating unknown parameters in PDEs, called PDE-Informed Gaussian Process Inference (PIGPI). Through modeling the PDE solution as a Gaussian process (GP), we derive the manifold constraints induced by the (linear) PDE structure such that under the constraints, the GP satisfies the PDE. For nonlinear PDEs, we propose an augmentation method that transfers the nonlinear PDE into an equivalent PDE system linear in all derivatives that our PIGPI can handle. PIGPI can be applied to multi-dimensional PDE systems and PDE systems with unobserved components. The method completely bypasses the numerical solver for PDE, thus achieving drastic savings in computation time, especially for nonlinear PDEs. Moreover, the PIGPI method can give the uncertainty quantification for both the unknown parameters and the PDE solution. The proposed method is demonstrated by several application examples from different areas.