How the brain works is one of the most mysterious yet challenging problems in life sciences. Understanding the molecular and neural basis of cognition and memory is expected to not only aid the exploration of the pathogenesis of neurological and neuropsychiatric disorders but also provide the fundamental principles for brain-inspired intelligence. Various neural technologies are continuously developed to provide tools for resolving this ultimate biological problem. Such technologies include molecular genetic tools (particularly genetically encoded calcium indicators and viral trans-synaptic labeling vectors) that images neural circuit activities and neuro-anatomy. CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system is a powerful molecular genetic tool that has revolutionized various scientific fields, especially genome editing, gene expression control, cellular imaging, and molecular tracing. In this review, we discuss the applications and limitations of CRISPR/Cas9 technology in neuroscience and provide possible directions and strategies for the advancement of CRISPR/Cas9 technology in studying the neural basis of cognition and memory.