The field of spatial cognitive training and evaluation has rapidly evolved. However, the low learning motivation and engagement of the subjects hinder the widespread use of spatial cognitive training. This study designed a home-based spatial cognitive training and evaluation system (SCTES), which aimed to train subjects on spatial cognitive tasks for 20 days, and compared the brain activities before and after the training. This study also evaluated the feasibility of using a portable all-in-one prototype for cognitive training that combined a virtual reality (VR) head-mounted display with high-quality electroencephalogram (EEG) recording. During the course of training, the length of the navigation path and the distance between the starting position and the platform position revealed significant behavioral differences. In the testing sessions, the subjects showed significant behavioral differences in the time it took to complete the test task before and after training. After only four days of training, the subjects demonstrated significant differences in the Granger causality analysis (GCA) characteristics of brain regions in the delta ,theta, alpha(1), beta(2), and gamma frequency bands of the EEG, as well as significant differences in the GCA of the EEG in the beta(1), beta(2), and gamma frequency bands between the two test sessions. The proposed SCTES used a compact and all-in-one form factor to train and evaluate spatial cognition and collect EEG signals and behavioral data simultaneously. The recorded EEG data can be used to quantitatively assess the efficacy of spatial training in patients with spatial cognitive impairments.