Studies have found that electroacupuncture (EA) can improve the neurocognitive function of cerebral small vessel disease (CSVD), restore cerebral blood flow, and protect neurovascular units. The occurrence and development of cerebral microvascular disease is highly related to neurovascular unit injury. However, it is not clear whether EA plays a therapeutic role by restoring neurovascular unit injury. To explore the possible therapeutic mechanism of EA by analyzing its effect on CSVD neurovascular units in rats with CSVD. Adult male Sprague–Dawley rats (n = 36) were used for the experiment. The rat model of bilateral carotid artery occlusion (BCAO) was established by bilateral common carotid artery ligation. The treatment group was treated with 2/100 Hz and 2–4 V continuous wave EA every day for 7 days. The water maze test and new object recognition test were used to evaluate the memory and cognition of rats. Golgi staining was performed to evaluate the synaptic plasticity. Western blotting was used to evaluate the expression of synaptic-associated proteins PSD95 and synaptophysin and neurovascular unit-associated proteins VEGF, NeuN, GFAP, and claudin5. The expression of neurovascular unit associated proteins VEGF, NeuN and GFAP was further evaluated by immunofluorescence staining. EA intervention significantly reduced cognitive memory damage, restored neuronal synaptic plasticity, and reduced neurovascular unit damage. EA significantly shortened the latency in the water maze test (p < 0.01), increased the number of platform crossings (p < 0.01) and the mean speed (p < 0.01), and increased new object recognition index (p < 0.01). EA significantly increased the total length of neuronal dendrites (p < 0.01) and the dendrite spinous density (p < 0.01). EA increased the levels of PSD95, Synaptophysin, VEGF, NeuN, GFAP and Claudin5 in the EA + BCAO group, compared with the BCAO group (p < 0.01). EA could improve the neurological function in a rat model of cerebral small vessel disease, and its mechanism may be related to the protective effect of electroacupuncture on neurovascular units.