The COVID-19 pandemic has lasted from 2019 to 2022, severely disrupting human health and daily life. The combined effects of spatial, environmental, and behavioral factors on indoor COVID-19 spread and their interactions are usually ignored. Especially, there is a lack of discussion on the role of spatial factors in reducing the risk of virus transmission in complex and diverse indoor environments. This paper endeavours to summarize the spatial factors and their effects involved in indoor virus transmission. The process of release, transport, and intake of SARS-CoV-2 was reviewed, and six transmission routes according to spatial distance and exposure way were classified. The triangular relationship between spatial, environmental and occupant behavioral parameters during virus transmission was discussed. The detailed effects of spatial parameters on droplet-based, surface-based and air-based transmission processes and virus viability were summarized. We found that spatial layout, public-facility design and openings have a significant indirect impact on the indoor virus distribution and transmission by affecting occupant behavior, indoor airflow field and virus stability. We proposed a space-based indoor multi-route infection risk assessment framework, in which the 3D building model containing detailed spatial information, occupant behavior model, virus-spread model and infection-risk calculation model are linked together. It is also applicable to other, similar, respiratory infectious diseases such as SARS, influenza, etc. This study contributes to developing building-level, infection-risk assessment models, which could help building practitioners make better decisions to improve the building’s epidemic-resistance performance.