Combined exercise and cognitive training have been evidenced to be effective in cognitive and physical functions in post-stroke survivors. Recent interest has gradually shifted to technology-aided cognitive rehabilitation. However, clear neural makers or comprehensive behavioral indexes used for evaluating rehabilitation remain unexplored. The study aimed to examine the effects of two types of combined exercise-cognitive training on stroke patients with cognitive dysfunction, focusing on neural and behavioral markers. 39 patients were randomly assigned to sequential exercise-cognitive training, simultaneous exercise-cognitive training or active control groups and underwent 60 minutes/day training, 3 days/week, for 12 weeks. 29 patients ultimately completed the training. The markers/indexes included cognitive function, physical function, instrumental activities of daily living, and caregiver strain. Cognitive function included working memory task performance, neurophysiological markers, and cognitive indexes. The results indicated no d-prime difference between groups after the training. The simultaneous training demonstrated significant improvements in the neurophysiological marker of P300 and theta coherence compared to the other groups. Moreover, the simultaneous training also led to significant enhancements in physical function, as measured by the Rivermead Mobility Index, comparing to the other groups. Further analysis contrasting the two exercise-cognitive trainings revealed that improvements in cognition and multifaceted domains (i.e., instrumental activities of daily living and caregiver strain) were manifested in the simultaneous training. Together with the neural markers identified in the current interventions, the differential impacts of the two interventions indicates the potential of technology-driven and personalized rehabilitation in post-stroke patients.