Existing numerical methods for fractional PDEs suffer from low accuracy and inefficiency in dealing with three-dimensional problems or with long-time integrations. We develop a unified and spectrally accurate Petrov–Galerkin (PG) spectral method for a weak formulation of the general linear Fractional Partial Differential Equations (FPDEs) of the form 0Dt2τu+∑j=1dcj[ajDxj2μju]+γu=f, where 2τ, μj∈(0,1), in a (1+d)-dimensional space–time domain subject to Dirichlet initial and boundary conditions. We perform the stability analysis (in 1-D) and the corresponding convergence study of the scheme (in multi-D). The unified PG spectral method applies to the entire family of linear hyperbolic-, parabolic- and elliptic-like equations. We develop the PG method based on a new spectral theory for fractional Sturm–Liouville problems (FSLPs), recently introduced in Zayernouri and Karniadakis (2013). Specifically, we employ the eigenfunctions of the FSLP of first kind (FSLP-I), called Jacobi poly-fractonomials, as temporal/spatial bases. Next, we construct a different space for test functions from poly-fractonomial eigenfunctions of the FSLP of second kind (FSLP-II). Besides the high-order spatial accuracy of the PG method, we demonstrate its efficiency and spectral accuracy in time-integration schemes for solving time-dependent FPDEs as well, rather than employing algebraically accurate traditional methods, especially when 2τ=1. Finally, we formulate a general fast linear solver based on the eigenpairs of the corresponding temporal and spatial mass matrices with respect to the stiffness matrices, which reduces the computational cost drastically. We demonstrate that this framework can reduce to hyperbolic FPDEs such as time- and space-fractional advection (TSFA), parabolic FPDEs such as time- and space-fractional diffusion (TSFD) model, and elliptic FPDEs such as fractional Helmholtz/Poisson equations with the same ease and cost. Several numerical tests confirm the efficiency and spectral convergence of the unified PG spectral method for the aforementioned families of FPDEs. Moreover, we demonstrate the computational efficiency of the new approach in higher-dimensions e.g., (1+3), (1+5) and (1+9)-dimensional problems.