The space division multiplexing elastic optical networks (SDM-EONs) based on multi-core fiber (MCF) are an effective solution to improve transmission capacity. In SDM-EONs, spectrum resources take on three-dimensional (3D) properties (i.e., frequency, time, and space), which brings new spatial constraints to network resource allocation. Meanwhile, the spectrum fragmentation in the network also present same characteristics with the setup and release of dynamic lightpath. To improve the success rate of transmission and the utilization of network resources, it is necessary to evaluate network fragmentation effectively from the three dimension. Therefore, this paper focuses on a new fragmentation measurement for SDM-EONs. Firstly, the 3D fragmentation metric is carried out considering the frequency-time-space domain. Then, routing, core, and spectrum allocation (RCSA) scheme is proposed to allocate the spectrum resource with minimal future fragmentation and core resource with maximal free resource reservation. Simulation results show the proposed scheme better in blocking probability, spectrum utilization, and fragmentation rate.