Internal short circuit in lithium-ion battery by penetrating element leads to exothermic behavior due to accumulated heat. In the present study, investigations are conducted on the thermal behavior of the LIR2450 micro coin cell haivng capacity of 120 mAh, with internal short circuit by penetrating element. The experimental coin cell discharge study was conducted and validated with numerical study within ±5.0%. The effect of penetrating element size, location of penetrating element, state of charge, discharge rate, short-circuit resistance, and heat transfer co-efficient on maximum coin cell temperature and heat generation rate are analyzed. The penetrating element diameters of 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, and 3.5 mm are considered. The effect of initial state of charge (SOC) is considered with 100%, 80%, 60%, and 40%. Three locations for penetrating element are considered with the center, the middle of the radius, and on the edge of the coin cell radius. The different discharge rates of 1C, 2C, 3C, and 4C are considered. The higher-penetrating element size of 3.5 mm with location at the center of the coin cell with 100% SOC showed maximum heat generation rate and maximum temperature of the coin cell. In addition, the optimum value of the dimensionless heat generation rate is obtained at dimensionless short-circuit resistance. The study provides comprehensive insights on the thermal behavior of the lithium-ion cell during thermal abuse condition with internal short circuit by penetrating element.