In three-phase inverters used in uninterruptible power supplies (UPSs), three-limb inductors and three-limb transformers are commonly used in consideration of cost and size. However, magnetic coupling exists between the three phases of the inverter, which can result in complex models. When instantaneous feedback control strategies are introduced to achieve high quality output waveforms, the transient analysis of the closed-loop inverters becomes difficult. In this paper, the phenomenon of magnetic coupling in three-phase inverters due to three-limb inductors and three-limb transformers is analyzed. A decoupled dynamic model is derived based on the instantaneous symmetrical components transformation, which comprises three decoupled equivalent circuits of instantaneous symmetrical components. Analyses based on this model indicate that magnetic coupling may have a significant impact on the performance of three-phase inverters under unbalanced load conditions and transient responses. For three-phase inverters in UPSs with Proportional-Integral-Differential (PID) closed-loop control strategies, the interactive influence between instantaneous closed-loop regulation and magnetic coupling is researched. Finally, a method of reliability analysis and PID controller design for inverters with magnetic coupling is derived. Simulation and experiment results validate the model and conclusions.