The simple circuit based on DC-DC converters is the main attractive feature of the differential inverter topologies. It has a single-stage and provides modularity and scalability. However, the Negative Sequence Harmonic Component (NSHC) generated at the output terminal may hinder its practical applications. This paper presents a single-stage three-phase isolated differential inverter based on three High-Frequency Link (HFL) transformer-based DC-DC SEPIC converters. The utilized SEPIC converters perform voltage step-up/ down capability with galvanic isolation, which is essential for Renewable Energy Sources (RES). It mitigates the Common-Mode Voltage (CMV) and ElectroMagnetic Interference (EMI). Moreover, this paper proposes a two-loop based d-q synchronous frame grid-current control to mitigate its NSHC. A Type-II compensator and simple NSHC detection circuit are proposed to enhance the inverter's stability and compensate phase-delay of the utilized SEPIC converters. NSHC detection is developed using three cascaded Low Path Filters (LPFs). A 1.6kW inverter prototype was set to validate the performance of the proposed inverter and its control. The control is implemented by the MWPE3 C6713A Expert III DSP board. The proposed topology has a maximum efficiency of 89.744 at 700W output power and 86.4% at full power. The proposed control decreases the NSHC from 40.6 % to 1.614%, which shows its accuracy and precision. Furthermore, THD is reduced from 35.61% to 4.087% and satisfy the recent grid codes (<5%). The simulation results using PSIM software, power loss distribution, and a comparison study of the proposed inverter with similar topologies are also presented.