Jojoba (Simmondsia Chinensis Schneider), the sole species in the Simmondsiaceae family, holds significant economic value. Understanding the mechanism of seed germination and post-germination is essential for jojoba breeding programs. For the first time, this study employed matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to comprehensively detect and image endogenous lipids in jojoba seeds during germination and post-germination. Meanwhile, a new method of lithium salt-doped 2-mercaptobenzothiazole (2-MBT) matrix was adopted to detect the wax ester in jojoba seeds. The spatial lipidomic analysis of MALDI-MS revealed the dynamics of lipid alterations during three stages of jojoba seed (stage I, quiescent seed; stage II, germination; stage III, post-germination). MALDI-MSI results demonstrated heterogeneous distributions of differential lipids and main wax esters (WEs) in unique tissue regions of the jojoba seed at different stages. For instance, at stages II and III, three phosphatidylcholines (PCs) (PC(36:2), PC(36:4), and PC(35:3)) are mainly localized in the cotyledons, while the other two PCs (PC(34:1) and PC(36:1)) were distributed in both cotyledons and embryonic axis. In contrast, three phosphatidylethanolamines (PE(36:1), PE(42:4), and PE(42:9)) are primarily distributed near the embryonic axis and phosphatidylserine (PS(32:0)) was found exclusively in the embryonic axis area at three stages. In addition, three phosphatidic acids (PA(40:7), PA(46:2), and PA(42:1)) displayed highly accumulated in the middle of the cotyledons at stages II and III. Besides, WEs are continuously degraded mainly in the cotyledons during germination and post-germination processes. This study offers new insights into lipid alterations from a spatial lipidomics perspective and can contribute to our understanding of the role of these specific lipids during jojoba seed germination and post-germination. These findings will deepen our understanding of the metabolic processes involved in jojoba seed germination and seedling development and have underlying implications for crop improvement and seed quality control.