Glow-plasma is a non-thermal physical technique and has gain huge interest in polymer modification due to the concerns over generated wastes and safety issues resulting from chemical modification. As the major storage carbohydrate in higher plants, starch is one of the most important raw materials for food and non-food industries. To improve the performance of starch and extend its applications, it is indispensible to understand how a specific technique alters the structure–property of starch. Regarding this, the present work revealed that the oxygen or helium glow-plasma preferably disorganized the crystallites of cassava starch with low perfection and thermal stability, which resulted in decreases in the relative crystallinity and the transition enthalpy but increases in the transition temperatures together with a narrowed transition temperature range. The thermal behavior of cassava starch could be further regulated by changing the gas type and the treatment time. These findings are much different from a previous work which showed if glow-plasma disorganized the supramolecular structure of starch, its thermal transition temperatures would be reduced. Hence, this study enables an understanding of how glow-plasma modulates the thermal property of cassava starch from a structural view, which is of value for rationally using glow-plasma as a new method to regulate the thermal transition of starch, for the production of starchy food products with desired thermal behavior.