Global warming has led to frequent high-temperature heatwave events in urban areas, increasing health risks in human habitats. This study focuses on aging residential buildings in hot and humid regions, where the problem is more pronounced, aims to diagnose the spatial–temporal distribution of indoor thermal environments and propose health-centric retrofit strategies. The study methodology integrates literature review and physical environment simulation, it reviews the relevant index requirements for thermal environments in health building standards both domestically and internationally. Additionally, the Ladybug + Honeybee physical environment simulation method is used to analyze the thermal and humidity conditions in a typical row-type, multi-story 1980s residential building in Shenzhen. Spatial–temporal analysis is conducted across floors, orientations, and functional rooms under natural ventilation, focusing on temperature, humidity, and PMV indices. The result reveals severe overheating in upper-floor and south/west-facing rooms, with peak temperatures reaching 36.2 °C due to solar radiation and roof heat transfer. Ground-floor rooms exhibited prolonged high humidity (>80%), elevating mold risks. Based on this, a hierarchical retrofit framework is proposed including improvement of thermal insulation and mold resistance of the envelope, improvement of natural ventilation design and introduction of passive cooling technology and intelligent control systems. The study establishes a replicable framework for health-centric retrofits in aging residential areas, advancing the “Healthy China 2030” agenda by addressing both energy efficiency and resident well-being.