Lavender plantation is globally expanded due to the increasing demand of its essential oil and its popularity as an ornamental species. However, lavender plantations, and consequently essential oil industries, are threatened by more frequent and severe drought episodes in a globally changing climate. Still little is known about the changes in the general metabolome, which provides the precursors of essential oil production, by extended drought events. Prolonged drought fundamentally results in yield losses and changing essential oil composition. In the present study, the general metabolome of a main cultivated lavender species (Lavandula angustifolia Mill.) in response to water deprivation (WD) and re‐watering was analyzed to identify the metabolomics responses. We found prolonged WD resulted in significant accumulations of glucose, 1,6‐anhydro‐β‐D‐glucose, sucrose, melezitose and raffinose, but declines of allulose, β‐D‐allose, altrose, fructose and D‐cellobiose accompanied by decreased organic acids abundances. Amino acids and aromatic compounds of p‐coumaric acid, hydrocaffeic acid and caffeic acid significantly accumulated at prolonged WD, whereas aromatics of cis‐ferulic acid, taxifolin and two fatty acids (i.e., palmitic acid and stearic acid) significantly decreased. Prolonged WD also resulted in decreased abundances of polyols, particularly myo‐inositol, galactinol and arabitol. The altered metabolite profiles by prolonged WD were mostly not recovered after re‐watering, except for branched‐chain amino acids, proline, serine and threonine. Our study illustrates the complex changes of leaf primary and secondary metabolic processes of L. angustifolia by drought events and highlights the potential impact of these precursors of essential oil production on the lavender industry.