Introduction & ObjectiveMechanical ventilation is a life‐saving intervention in patients with respiratory failure. Controlled mechanical ventilation (CMV) is the mode of mechanical ventilation used in patients with an insufficient central respiratory drive and frequently used in COVID‐19 patients ventilated in the prone position. However, CMV is also associated with negative consequences for the major respiratory muscle the diaphragm, i.e., the ventilator induced diaphragm dysfunction (VIDD). VIDD is the major factor underlying the delayed weaning from the ventilator especially in old intensive care unit (ICU) patients. The age‐related difference in mortality rate has become a major concern during the COVID‐19 pandemic. The current experimental study was undertaken to improve our understanding the mechanisms underlying age‐related differences in the response to CMV using a unique experimental ICU model allowing long‐term studies in a rat exposed CMV.Materials and MethodsYoung (7‐8 months) and old (28‐32 months) female F344 BN hybrid rats were exposed to the ICU condition for 5 days (anaesthetized, mechanically ventilated, and pharmacologically paralyzed by post‐synaptic blockade of the neuromuscular transmission). Transcriptomics (RNA‐Seq) and proteomics (Olink) analyses of the diaphragm and proteomics analysis of plasma were conducted to investigate the molecular differences between young and old rats exposed to the ICU condition.ResultsAccording to multi‐omics analyses, significant differences were observed in the diaphragm between young and old rats in response to ICU condition. In the diaphragm of young rats, CMV resulted in decreases in the biological processes related to energy metabolism and production as indicated by the downregulation of pathway like “glycolysis/gluconeogenesis”, “fatty acid metabolism”, “TCA cycle”, and “oxidative phosphorylation”, etc. On the other hand, in the diaphragm of old rats, dramatic immune and inflammatory responses were observed after CMV, as reflected in the upregulation of “Cytokine‐cytokine receptor interaction”, “TNF signaling pathway”, “IL‐17 signaling pathway”, etc. Transcriptomic results were consistent with plasma proteomics analyses, i.e., CMV induced a higher level of inflammatory factors and cytokines/chemokines in old rats.ConclusionsAfter 5‐days exposure to CMV, our multi‐omics study demonstrated age‐related inflammatory response to long‐term mechanical ventilation.Significance/ImplicationThus, CMV should be cautiously used and restricted to as short duration as possible, especially in the old patients. In the current COVID‐19 pandemic, the dramatically increased mortality in old ICU patients with COVID‐19‐associated hyperinflammation and cytokine storm need not only reflect the viral infection but may also be associated with the VIDD and hyperinflammatory responses induced by CMV per se.