Many severe air quality problems in the major cities of Southeast Asia (SEA) are related to atmospheric aerosols, and these are mainly caused by smoke haze from biomass burning. To better understand the cause and effect relationships for the tempo-spatial distributions of atmospheric aerosols in SEA, a variety of satellite-based Moderate Resolution Imaging Spectroradiometer (MODIS) products of aerosol optical depth (AOD), precipitation, burned area (BA) and fire pixel counts (FC, derived from the active fire product) were collected and processed to evaluate the spatial and temporal variations among atmospheric aerosol, climate factors, and biomass burning in SEA during 2002–2011. High AOD zones (HAZs) located in the continental and maritime portion of SEA are identified through hotspot analysis of AOD maps. The peak AOD, BA and FC months are concentrated in the dry seasons of each HAZ. Although BA and FC are mostly identified in Indochina, the HAZ located in maritime SEA has a comparable level of AOD which may be contributed by the fire-related emissions from peatland in Indonesia. Compared to the commonly used fire-effected area dataset (MCD45 product), BA derived from a hybrid approach (MCD64 product) that considers both active fire (AF) and land change information has higher correlation coefficients with AOD in both HAZs. Linear regression models are then developed for the Indochina and the maritime HAZs, to estimate the level of AOD from the MODIS monthly fire datasets. In general the empirical models can better explain the temporal trends of AOD in HAZs by using AF-based products. The links between regional aerosol and local burning in Indochina SEA are relatively complex due to the cross-boundary transport of aerosol from Southern China.