In this study, we investigated the effects of modified aging treatments on the microstructures and hardness in a commercial 6016 Al alloy through hardness tests and transmission electron microscopy (TEM) observations. The results demonstrate that many fine needle-like β″ phases contribute to the high hardness of peak-aged (T6) alloys. Over-aging treatments lead to the precipitation of lath-like β′, β″/disordered, or B′/disordered composite phases. Moderate over-aging treatment results in the coarsening of grain boundary precipitates (GBPs) and widening of the precipitate-free zone (PFZ), while heavy over-aging treatment triggers the re-precipitation of Cu-containing GBPs and increases the number density of GBPs. A retrogression and re-aging (RRA) treatment precipitates β″, lath-like β′, and disordered phases, while a two-step aging (T78) treatment precipitates β″, B′, and disordered phases. Both the T78 and the RRA treatments lead to the coarsening of GBPs and the widening of PFZs. The decreased hardness during over-aging treatments is attributed to a combination of coarsening intragranular precipitates and/or wider PFZs. The T78 and RRA tempers achieve 95.5% and 94% of the hardness values of the T6 treatment, respectively. The hardness values of the RRA and T78 treated alloys are related to the finer nano-sized precipitates formed during the high temperature process. These precipitates can compensate for the loss of hardness caused by the increase in the widths of the PFZs and the coarsening of the matrix precipitates. The relationship between the hardness and microstructures such as PFZs and precipitates in the matrix during various heat treatments is elucidated.