Three-dimensional (3-D) super-resolution ultrasound microvessel imaging (SR-UMI) has been recently proposed to visualize 3-D microvasculature by overcoming the diffraction limited resolution in three spatial dimensions. However, 3-D SR-UMI suffers from high system complexity and sophisticated microbubble tracking mechanisms to account for 3D movement. To reduce the system complexity, methods such as row-column matrix, sparse array and micro-beamforming have been proposed to reduce the number of transmit/receive channel at the cost of degradation of image quality. In this study, a sub-aperture process is used to reduce the required received channel counts at the cost of slightly reducing the overall frame rate. For the microbubble tracking, two dimensional (2-D) bipartite graph-based tracking has been proposed to improve microbubble tracking performance for 2-D SR-UMI. This approach can reduce the background noise, improve the performance of super-resolution image, and stabilize the estimated micro-vessel flow speed. We extended the 2-D bipartite graph-based method to 3-D SR-UMI to reduce background noise and to improve the micro-bubble tracking performance. In this study, a flow channel phantom was used to evaluate the performance of the proposed method. Results showed that the proposed method can effectively improve the spatial resolution as compared with 3-D Power Doppler images.