Fabrication of bench-stable radical ions under ambient conditions is of utmost significance from the perspective of materials and structural (solid-state) chemistry. Two exceptionally stable benzotriazinyl radical cationic salts of 1-phenyl-3(phenylamino)-1,2,4-benzotriazin-4-ium-1-ylium (A and B) have been prepared and structurally characterized for the first time, in which the hydrogen bonding controls their supramolecular arrangement, and thus, their magnetism is exploited. Introduction of intrinsically disordered trifluoroacetate counteranion (A) leads to a reversible phase transition (PT) at ca. similar to 119 K, associated with order-disorder structural transformation of the magnetically innocent counteranion. In turn, no such transition was observed using a nondisordered 2-nitrobenzoate counteranion (B). Variable temperature crystallography along with molecular dynamics simulations quantitatively demonstrates that order-disorder structural transformation in A leads to a cooperative change in the dynamic motion of the radical pairs. Consequently, this changes the pi-pi stacking interactions (d) and latitudinal and longitudinal slippage angles phi) and modifies the distribution of the magnetic exchange couplings (J) in A upon thermal vibration. Overall, it is a demonstration of a new mechanism to introduce subtle molecular changes to regulate the magnetism of organic open shell components.