Objective To introduce an improved extraction method of prefrontal cortical and striatal synaptosomes from SHR rat. Methods Synaptosomes were prepared from SHR rat brain tissue by Percoll density gradient centrifugation. Transmission electron microscopy was used to assess the morphology and structural integrity of the synaptosomes. Results The obtained synaptosomes showed oval structures surrounded by an intact membrane. Presynaptic components contained one or more mitochondria and a large number of synaptic vesicles. The synaptic clefts were clearly visible, and prominent part of the characteristic compact structure was clear, complete and with higher electron-density. The synaptosome presynaptic membrane, synaptic cleft, and postsynaptic membrane were well preserved,and the synaptosomes were densely distributed, showing typical morphological characteristics of synaptosomes. Conclusions The results of our study improved the traditional preparation method and provide a less time-consuming, highly productive protocol for preparation of structurally typical and intact synaptosomes, suitable for further research on neuroscience and neurological diseases.