Foods rich in phosphatidic acid (PA) can ameliorate stomach ulcers in mice by hydrolysis of PA to lysophosphatidic acid (LPA). In this study, PA-rich komatsuna was produced using the micro wet milling (MWM) system, which can mill food products into micrometer-scale without causing detrimental factors such as frictional heat. To evaluate the efficiency of the MWM system in increasing PA and forming LPA, the availability of PA in the MWM komatsuna to hydrolyze into LPA under in vitro simulated gastrointestinal (GI) digestion conditions were investigated. The results showed that through effective MWM milling, komatsuna was sufficiently milled into smaller particles, and PA was abundantly produced in the milled komatsuna; the increased PA promoted LPA formation during digestion, resultant a dominant molecular species of 16:0 LPA which could effectively reduce ulcer lesions. These indicated that MWM can elevate the bioaccessibility of komatsuna PA and LPA in the GI tract, which will benefit the dietary treatment of stomach ulcers.