Effects of stirring during gelatinization and shaking during hydrolysis on physicochemical properties of short-chain glucan aggregates (SCGA) were investigated. Both stirring and shaking improved SCGA yield, and also affected the formation and crystallization kinetics of SCGA. Without stirring and shaking, slow SCGA forming rate, large size (∼1.32 μm), high relative crystallinity (RC), high endothermic onset temperature, and high melting enthalpy (ΔH) were observed. Stirring and shaking yielded the fastest SCGA formation and crystallization rates as well as the smallest SCGA size (∼0.57 μm). Small SCGA had a low RC and low heat stability, possibly due to the presence of imperfections and low double helix content. Formation yield was negatively correlated with size, ΔH, RC, and the resistant starch content of SCGA. The highest correlations were observed between ΔH and RC. This study proves that the SCGA characteristics can easily be controlled by stirring during gelatinization and shaking during enzymatic hydrolysis.