Emerging evidence indicates that ribosomes are regulated by various post-translational modifications to maintain proteostasis. However, the global landscape and functional impacts of lipid modification on ribosomes remain largely unexplored, due to technical limitations. Here, we present a simple, probe- and chemical-reaction-free workflow that enables global, site-resolved analysis of intact protein lipidation. Using this approach, we identify over 1,200 endogenous lipidation sites and simultaneously detect multiple lipid modifications, including myristoylation, palmitoylation, and prenylation, revealing hundreds of previously unreported lipidation events on diverse proteins. Applying this method to human ribosomes reveals an extensive landscape of long-chain S-acylation, with approximately 75% of cysteine-containing ribosomal proteins modified. Functional analysis shows that palmitoylation at cysteine 66 of RPS5/uS7 influences nuclear export of pre-40S ribosomes. These findings suggest a regulatory role for S-acylation in ribosome biology, offering new insights into the modulation of translation machinery through lipid modifications. We performed AirID-based proximitiy labeling proteomics.