Rhythmic abilities are impaired in developmental coordination disorder (DCD) but learning deficit of procedural skills implying temporal sequence is still unclear. Current contradictory results suggest that procedural learning deficits in DCD highly depend on learning conditions. The present study proposes to test the role of sensory modality of stimulations (visual or auditory) on synchronization, learning, and retention of temporal verbal sequences in children with and without DCD. We postulated a deficit in learning particularly with auditory stimulations, in association with atypical cortical thickness of three regions of interesting: sensorimotor, frontal and parietal regions. Thirty children with and without DCD (a) performed a synchronization task to a regular temporal sequence and (b) practiced and recalled a novel non-regular temporal sequences with auditory and visual modalities. They also had a magnetic resonance imaging to measure their cortical thickness. Results suggested that children with DCD presented a general deficit in synchronization of a regular temporal verbal sequence irrespective of the sensory modality, but a specific deficit in learning and retention of auditory non-regular verbal temporal sequence. Stability of audio-verbal synchronization during practice correlated with cortical thickness of the sensorimotor cortex. For the first time, our results suggest that synchronization deficits in DCD are not limited to manual tasks. This deficit persists despite repeated exposition and practice of an auditory temporal sequence, which suggests a possible alteration in audio-verbal coupling in DCD. On the contrary, control of temporal parameters with visual stimuli seems to be less affected, which opens perspectives for clinical practice.