In this paper, for synchronizing two actual nonidentical fractional-order hyperchaotic systems disturbed by model uncertainty and external disturbance, the fractional matrix and inverse matrix projective synchronization methods are presented and the methods' correctness and effectiveness are proved. Especially, under certain degenerative conditions, the methods are reduced to study the complete synchronization, antisynchronization, projective (or inverse projective) synchronization, modified (or modified inverse) projective synchronization, and stabilization problem for the disturbed (or undisturbed) fractional-order hyperchaotic systems. In addition, as the fractional matrix and inverse matrix projective synchronization methods' applications, the fractional-order hyperchaotic Chen and Rabinovich systems disturbed by model uncertainty and external disturbance are constructed, and the matrix and inverse matrix projective synchronizations between the two disturbed systems are achieved, respectively. This work constructs a basic theoretical framework of fractional matrix and inverse matrix projective synchronization methods and provides a general method for synchronizing the actual disturbed fractional-order hyperchaotic systems that are related to science and engineering. KEYWORDS disturbed hyperchaotic system, fractional inverse matrix projective synchronization, fractional matrix projective synchronization, fractional-order derivative Math Meth Appl Sci. 2018;41:6907-6920.wileyonlinelibrary.com/journal/mma