The first detailed description of the morphology of gastric ulcer was reported ~230 years ago, but the mechanism has yet to be elucidated. Moreover, peptic ulcers, including duodenal and gastric ulcers, are currently considered an infectious disease caused by Helicobacter pylori, but how the infection leads to ulceration remains elusive. To address these challenges, a recently published Complex Causal Relationship was applied to analyze the existing data. Peptic ulcers were identified as a psychosomatic disease triggered by psychological stress, where Helicobacter pylori plays a secondary role in only the late phase of the disease. This etiology explained all the characteristics and observations/phenomena of peptic ulcers in a series of 6 articles. This second article focused on the pathogenesis of gastric ulcers. Based on hereditary predisposition, the accumulation of past life experiences incurs the formation of a negative lifeview. Consequently, the individual tends to negatively evaluate themselves or current life events, leading to acute psychological stress. The psychological stress triggers the release of aberrant neurotransmitters in the central nervous system, which in turn cause the transmission of pathogenic nerve impulses to the stomach, resulting in a ‘pre-ulcer lesion’ in the gastric wall and eventually, gastric ulcer. This psychopathological model elucidated 12 characteristics and 24 observations/phenomena of gastric ulcer, along with the roles of gastric acid, Helicobacter pylori, and NSAIDs. The effectiveness suggests that theoretical research and empirical study are equally important in medical explorations, and the guiding roles of philosophy are indispensable for the major progress of life science and medicine.