The cathode material NaFePO of sodium-ion batteries exhibits complex phase segregation thermodynamics with the existence of an intermediate phase, and large volume change during (dis)charging. A virtual multiscale modeling chain is established to construct a 3D anisotropic electro-chemo-mechanical phase-field model based on first-principles calculations for NaFePO, which considers phase changes, electrochemical reactions, anisotropic diffusion, anisotropic misfit strain, and anisotropic elasticity, as well as the concentration-dependence of the elasticity tensor. The elastic properties of NaFePO are determined by first-principles for the first time. We investigate how surface reaction kinetics and crystal anisotropy influence the full 3D microstructure evolution, with results that include phase evolution, interface morphology, and stress evolution in NaFePO particles. We find that the existence of 1D Na diffusion channels leads to a kinetically arrested state of single wave propagation along [010]. Furthermore, defect-actuated in-plane diffusion induces low-energy single wave propagation along [100] controlled by the concentration dependent anisotropic elasticity tensor. In addition, the morphology of the double wave propagation along [010] is more prone to particle cracking and mechanical degradation. Beyond NaFePO, the findings of this work point towards opportunities to engineer desired phase behavior with better mechanical stability by defect-actuated out-of-1D diffusion of an intercalation electrode material.