The flexible and sophisticated movement of the gastrointestinal (GI) tract implies the involvement of mechanisms that are intellectually coordinating excitation in micro-regions other than the neural reflex. We thus performed image analysis of pacemaker micro-coordination in the small intestine of mice, which contains network-forming pacemaker cells. Field potentials were recorded by a dialysis membrane-reinforced microelectrode array (MEA). The micro-coordination of pacemaker activity varied considerably although four basic patterns were identified. Two major patterns of pacemaker activity were ′expanding′ and ′migrating′, defined as the initiation from and propagation to the MEA sensing area, respectively. The existence of ′expanding′ and ′migrating′ patterns were attributed to duplicated pacemaker current systems such as intracellular Ca2+ oscillation-activated and voltage-gated mechanisms. Consequently, these patterns reflect spontaneity and synchrony/continuity, respectively. The initiation region of ′expanding′ activity fluctuated while the direction of ′migrating′ activity changed, even reversibly. The ′bumpy′ pattern was characterized by spatiotemporal irregularity and was associated with local impairment of excitability, while the ′colliding/converging′ pattern involved the interaction of multiple activities in the MEA sensing area. Therefore, both represent the disruption of synchrony/continuity. Interconversion between the four micro-coordination patterns occurred in the same area. 5-Hydroxytryptamine (5-HT) promoted ′migrating′ activity, accompanied by decreases in ′bumpy′ and ′colliding′ events, implying an improvement/restoration of spatial conductivity. These results agree well with the action of 5-HT to change GI movement toward propulsion. In conclusion, our MEA method of image classification enables the quantitative assessment of spatio-temporal excitation underlying GI motility, and is especially useful in small model animals.