Net-zero energy homes (NZEHs) have been studied widely from different perspectives to provide realistic and practical solutions. Among various approaches to enable NZEH designs, energy-efficient heating, ventilation, and air-conditioning (HVAC) systems play a key role in providing thermal comfort and good air quality in a cost- and energy-efficient manner. This study proposes a NZEH design using photovoltaic (PV)-based distributed energy generation and multi-functional variable refrigerant flow (VRF) systems with electric and thermal energy storage systems. Simulation-based NZEH performance evaluation is conducted based on case studies under various US climate conditions. To develop a validated NZEH simulation model, the net-zero energy residential test facility (NZERTF) constructed by the US National Institute of Standards and Technology (NIST) is used for benchmarking the NZEH reference model. Changes in monthly energy consumption and on-site power generation before and after the VRF application are analyzed to capture the potential impact of the VRF system application for the NZEH design. This study shows that the alternative NZEH design with the proposed VRF and electric and thermal energy storage systems can achieve around 13% through 32% of cooling energy reductions under different US climate conditions. With the proposed VRF system, the savings potential of domestic hot water energy consumption is significant up to 90% reduction compared to the original NZEH before the proposed VRF and energy storage systems were considered.