The lack of intra-continental air connectivity in Africa has long been criticized. This paper aims to understand the factors determining intra-regional air transportation in the Southern Africa region and the impact of the COVID-19 pandemic. Firstly, we analyze the geospatial characteristics of the air transport network, airport connectivity, and market structure before and after the pandemic. We also examine the progress of air transport liberalization in Africa and its impact on market structure and airline privatization. We find that the liberalization facilitated market competition and the progress of privatization, but its influence didn’t sustain long. Secondly, based on monthly data at the city level from April 2012 to December 2021, using monthly Total Night-time Light Intensity (TNLI) as a proxy of gross regional product (GRP), we develop a gravity model to empirically investigate the determinants of international air passenger flows within Southern Africa. The analysis shows that the factors promoting air traffic include GRP, air transport liberalization, the presence of low-cost carriers, and airline privatization, while high market concentration and diplomatic disagreements hinder air passenger flows. The pandemic and associated government restriction measures have severely impacted intra-regional air transport connectivity, while the vaccination program has significantly contributed to the recovery of air transportation.