Net-zero energy building (NZEB), an initiative to address energy conservation and emission reduction, has received widespread attention worldwide. This study aims to systematically explore recent challenges in NZEB retrofit research through a mixed-method approach and provide recommendations and future directions. A review of 106 documents (2020–2024) retrieved from the Web of Science and Scopus databases found that the globalization of NZEB retrofit research is unstoppable. Assessment methods are diverse, ranging from modeling energy efficiency (using different software such as DesignBuilder 7.0, PVsyst 7.4, EnergyPlus 24.1.0, etc.) to multi-attribute decision-making methods (e.g., DEMATEL-AHP/ANP-VIKOR) and comparative analysis. Current assessment metrics are dominated by economic benefits (e.g., net present value, dynamic payback period, and total operating cost) and energy consumption (e.g., electricity consumption and generation), with less consideration of environmental impacts (e.g., carbon reduction), as well as comfort (e.g., thermal comfort and indoor comfort). The study found that current challenges mainly include “Low economic feasibility of retrofitting”, “Building retrofit energy code irrationality”, and “Insufficient understanding, communication, and trust between stakeholders”. To overcome these challenges, the study also proposes a framework of strategies to address them, including (1) maximizing natural space, (2) introducing a tenant equity system, (3) upgrading waste management, (4) strengthening energy monitoring, (5) establishing complete life cycle mechanisms, (6) providing systemic solutions; (7) promoting the use of low-carbon building materials, and (8) increasing policy support.