There has been a growing interest in the association between indoor air quality (IAQ) with an increase in the time spent at home. However, there is still a lack of evidence on the impact of IAQ on occupants' health and well-being in the long term. This study aimed to develop a field-based longitudinal study design to evaluate the IAQ level and daily symptoms of adults and children living in different types of buildings over one year. We proposed vital principles to be considered when recruiting the study participants so that potential confounders, such as age, underlying diseases, and the geographic area would be either removed in advance or matched between different building types. We suggested collecting exposure and outcome data in three categories: lifestyle and housing environment, IAQ measurement, and occupants' health. We presented web-based survey tools for collecting housing and health data, and the frequency of data collection varied from weekly to six-month intervals. We developed two different models using a generalized mixed model for modeling the association between housing environment, IAQ, and human health. The current study design could be applied for future studies on the association between built environment and health, regardless of the type of buildings.•A real-time indoor air quality monitor was used to monitor indoor air parameters every 5 mins over one year.•A simple web-based survey tool was developed to collect data for occupants' daily symptoms in the long term.•A binomial generalized linear mixed model and a Poisson generalized linear mixed model was developed to evaluate the association between indoor air parameters, and building types and daily symptoms.