Objective To explore the effects of CDP-diacylglycerol synthase 1 (CDS1) on autophagy and amyloid deposition in hippocampal neurons of mice and the related mechanism. Methods Congo red and immunohistochemical staining were used to observe the amyloid deposition in hippocampus of amyloid precursor protein (APP)/presenilin 1 (PS1) double-transgenic mice. Lentivirus-mediated overexpression of APP was induced in HT22 cells, and Congo red staining was used to observe the amyloid deposition in HT22 cells. The protein expression levels of microtubule-associated protein 1 light chain 3 (LC3)-Ⅱ and P62 in the hippocampus of APP/PS1 double-transgenic mice and APP-overexpressed HT22 cells were detected by Western blotting. The differential protein CDS1 was screened based on the hippocampal proteomics results of APP/PS1 double-transgenic mice. The expression of CDS1 protein in hippocampal tissue of APP/PS1 transgenic mice and APP-overexpressed HT22 cells was detected by Western blotting. After lentivirus-mediated APP overexpression in HT22 cells, CDS1 was overexpressed, and the protein expression levels of LC3-Ⅱ and P62 were detected by Western blotting. Results β-amyloid protein (Aβ) was deposited in the hippocampus of APP/PS1 mice and in HT22 cells overexpressing APP. The levels of LC3-Ⅱ and P62 protein in the hippocampus of APP/PS1 double-transgenic mice and APP-overexpressed HT22 cells were significantly increased. A differential metabolic pathway, glycerophospholipid metabolic pathway, was screened by Kyoto Encyclopedia of Genes and Genomes pathway analysis in the proteomic results of APP/PS1 double-transgenic mice, and the differential protein CDS1 was obtained. Compared with wild-type C57BL/6 mice, APP/PS1 double-transgenic mice exhibited a significantly decrease in CDS1 protein expression in the hippocampus (0.46±0.07 vs 1.00±0.25, P＜0.01). Similarly, lentivirus-mediated overexpression of APP in HT22 cells resulted in decreased CDS1 protein levels compared to cells infected with empty viral vector controls (0.68±0.18 vs 1.00±0.13, P＜0.01). The autophagy flow of nerve cells was significantly restored after the CDS1 overexpression in APP-overexpressed HT22 cells (LC3-Ⅱ: 1.00±0.15 vs 0.21±0.05, P＜0.01; P62: 1.00±0.16 vs 0.67±0.10, P＜0.01), and Aβ deposition was significantly decreased. Conclusion Downregulation of CDS1 expression can induce dysfusion of autophagosome and lysosome, promoting amyloid deposition in hippocampus of mice with Alzheimer’s disease.