Tuning the properties of magnetic topological materials is of interest to realize exotic physical phenomena, new quantum phases and quasiparticles, and topological spintronic devices. However, current topological materials exhibit Curie temperature (TC) values far below those needed for practical applications. In recent years, significant progress has been made to control and optimize TC, particularly through defect-engineering of these structures. Most recently, we reported TC values up to 80 K for (MnSb2Te4)x(Sb2Te3)1−x when 0.7 ≤ x ≤ 0.85 by controlling the composition x and the Mn content in these structures during molecular beam epitaxy growth. In this study, we show further enhancement of the TC, as high as 100 K, by maintaining high Mn content and reducing the growth rate from 0.9 nm/min to 0.5 nm/min. Derivative curves of the Hall resistance and the magnetization reveal the presence of two TC components contributing to the overall value and suggest TC1 and TC2 have distinct origins: excess Mn in MnSb2Te4 septuple layers (SLs) and high Mn content in Sb2−yMnyTe3 quintuple layer (QL) alloys, respectively. To elucidate the mechanisms promoting higher TC values in this system, we show evidence of enhanced structural disorder due to the excess Mn that occupies not only Sb sites but also Te sites, leading to the formation of a new crystal structure for these materials. Learning to control defects that enhance desired magnetic properties and understanding the mechanisms that promote high TC in magnetic topological materials such as (Mn1+ySb2−yTe4)x(Sb2−yMnyTe3)1−x is of great importance to achieve practical quantum devices.