Lipid oxidation is involved in various biological phenomena (e.g., oxylipin generation and oxidative stress). Of oxidized lipid structures, the hydroperoxyl group position of lipid hydroperoxides (LOOHs) is a critical factor in determining their biological roles. Despite such interest, current methods to determine hydroperoxyl group positions possess some drawbacks such as selectivity. While we previously reported mass spectrometric methods using Na for the highly selective determination of hydroperoxyl group positions, nothing was known except for the fact that sodiated LOOHs (mainly linoleate) provide specific fragment ions. Thus, this study was aimed to investigate the effects of different alkali metals on the fragmentation of LOOHs, assuming its further application to analysis of other complex LOOHs. From the analysis of PC 16:0/18:2;OOH (phosphatidylcholine) and FA 18:2;OOH (fatty acid), we found that fragmentation pathways and ion intensities largely depend on the binding position and type of alkali metals (i.e., Li, Hock fragmentation; Na and K, α-cleavage (Na > K); Rb and Cs, no fragmentation). Furthermore, we proved that this method can be applied to determine the hydroperoxyl group position of esterified lipids (e.g., phospholipids and cholesterol esters) as well as polyunsaturated fatty acids (PUFAs) including n-3, n-6, and n-9 FA. We anticipate that the insights described in this study provide additional unique insights to conventional lipid oxidation research.