Ensuring rotor stability is a major concern in engineering, as instabilities can lead to catastrophic failures. Existing literature shows that anisotropic boundary conditions significantly affect the parametric instability characteristics of rotors under periodical axial loads. However, there is little literature systematically analyzing the formation mechanism of parametric resonance under these boundary conditions or providing a detailed classification of the parametric instability regions. Therefore, this paper presents a comprehensive parametric instability analysis of a rotor subjected to periodic axial loads under anisotropic boundary conditions. A novel approach based on the multiple scales method is proposed to address anisotropy in the boundary conditions. Using this approach, the analytical boundaries of the parametric instability regions are derived, and a proof regarding the absence of certain parametric resonances is presented. These analytical solutions are validated by numerical results obtained from the discrete transition matrix method, which form the basis for systematically investigating the effects of anisotropy in direct or cross-coupling stiffness/damping coefficients on the rotor instability. The key scientific contributions of this work include: Deriving analytical instability boundaries, providing a more efficient alternative to purely numerical methods while maintaining high accuracy; Demonstrating the absence of parametric resonance of difference type under both isotropic or anisotropic boundary conditions; Discovering that anisotropy in stiffness coefficients can induce self-interaction within a given forward or backward whirl mode, as well as interaction between two forward or two backward whirl modes, leading to additional instability regions; Reducing anisotropy in direct damping coefficients may increase critical dynamic load coefficients, potentially enhancing rotor safety; If the cross-coupling stiffness coefficients exceed the threshold for triggering intrinsic instability, the rotor may become unstable in all operating conditions. All these findings offer insights into the stability management of rotors under various operating conditions and provide valuable guidance for designing and operating safer, more efficient rotor systems.