Abnormal deposition of amyloid-β (Aβ) in the deep-brain hippocampus can impair synaptic transmission and disrupt neural network activity, thereby inducing learning and memory deficits and accelerating cognitive decline in Alzheimer’s disease (AD). Therefore, reducing hippocampal Aβ deposition is an important strategy for delaying AD progression. Existing transcranial electrical stimulation methods are limited by safety thresholds and are difficult to achieve effective field strength in deep brain regions under noninvasive conditions, thus failing to effectively intervene in hippocampal Aβ deposition. Nanosecond pulsed electric fields, which contain abundant high-frequency components and exhibit stronger transcranial penetration capability, may overcome this limitation. In this study, nanosecond transcranial pulsed electric field stimulation (ns-tPFS) was applied with parameters of 500 ns band width, 500 V amplitude, and 5 Hz frequency in a five familial AD mutations (5xFAD) mouse model. First, finite element simulation was performed to determine that the electric field strength generated by ns-tPFS in the hippocampal region could reach 3 × 104 V/m. Then, molecular dynamics simulation was used to evaluate the disruptive effect of this field strength on the structural stability of Aβ multimers. Subsequently, Morris water maze and Y-maze behavioral tests, together with immunofluorescence detection, were conducted to assess the intervention effects of ns-tPFS on animal cognitive function and hippocampal Aβ deposition. The results showed that, under the above stimulation parameters, ns-tPFS could disrupt the structure of Aβ multimers, markedly reduce hippocampal Aβ deposition in 5xFAD mice, and effectively improve their cognitive function. In summary, this study demonstrates, from animal simulations and experiments, the feasibility of ns-tPFS for improving AD symptoms and provides a new research perspective and experimental basis for the noninvasive intervention of hippocampal Aβ pathology.