[Backround] After stroke, injured axons can not ordinarily regenerate. The limited ability for axon regeneration is partly attributed to the inhibitory extrinsic environment such as inflammatory reaction. Inflammation has been supposed to be both detrimental and beneficial in the central nervous system (CNS) lesion, but the true feature is still veiled under conventional modality. The aim of this study is to use imaging mass spectrometry (IMS) to profile the state after selective white matter injury (WMI) rat model. [Materials and methods] Sprague-Dawley rats (300-350g, total n=30) were anesthetized, endothelin-1 was stereotactically injected into unilateral internal capsule to induce selective WMI. Animals were euthanized at several time points and brain section was analyzed. After conventional histopathological evaluation, the adjacent section was applied for IMS to analyze PCs comprehensively. [Results] Selective WMI was confirmed by specific APP immunoreactivity. The increased immunoreactivitiy for ED1 was observed in the lesion from 3 days to 2 weeks after injection, showing the activated microglia migrated and occupied the lesion. Notably, IMS revealed that PCs containing arachidonic acid, such as PC (16:0/20:4), as well as lysophosphatidylchoines (LPCs), especially LPC (16:0), were significantly elevated concomitant with the increased ED1 immunoreactivity in the lesion. [Discussion] Once the insult occurs in CNS, the microglia is known to activate, change their own shape, migrate to the lesion and secrete mediators such as cytokines and prostanoids. The increase of PCs containing arachidonic acid, containing a kind of polyunsaturated fatty acid which is key components of cell membrane, may represent the morphological change of microglia. Furthermore, increased LPCs indicate release of arachidonic acid and production of prostaglandins. In conclusion, IMS has tremendous potentials to provide the new insight comprehensively in terms of the dynamic molecular changes invisible under conventional modality and inflammation phase after white matter injury may be the therapeutic target for stroke recovery.