Memristor devices are generally suitable for incorporation in neuromorphic systems as synapses because they can be integrated into crossbar array circuits with high area efficiency. In the case of a two-dimensional (2D) crossbar array, however, the size of the array is proportional to the neural network's depth and the number of its input and output nodes. This means that a 2D crossbar array is not suitable for a deep neural network. On the other hand, synapses that use a memristor with a 3D structure are suitable for implementing a neuromorphic chip for a multi-layered neural network. In this study, we propose a new optimization method for machine learning weight changes that considers the structural characteristics of a 3D vertical resistive random-access memory (VRRAM) structure for the first time. The newly proposed synapse operating principle of the 3D VRRAM structure can simplify the complexity of a neuron circuit. This study investigates the operating principle of 3D VRRAM synapses with comb-shaped word lines and demonstrates that the proposed 3D VRRAM structure will be a promising solution for a high-density neural network hardware system.