Beyond diagonal reconfigurable intelligent surfaces (BD-RIS) have emerged as a transformative technology for enhancing wireless communication by intelligently manipulating the propagation environment. Its interconnected elements offer enhanced control over signal redirection, making it a promising solution for integrated terrestrial and non-terrestrial networks (NTNs). This paper explores the potential of BD-RIS in improving cognitive radio enabled multilayer non-terrestrial networks. We formulate a joint optimization problem that maximizes the achievable spectral efficiency by optimizing BD-RIS phase shifts and secondary transmitter power allocation while controlling the interference temperature from the secondary network to the primary network. To solve this problem efficiently, we decouple the original problem and propose a novel solution based on an alternating optimization approach. Simulation results demonstrate the effectiveness of BD-RIS in cognitive radio enabled multilayer NTNs.