A method and a system for detecting resistance of an internal short circuit of a battery are provided. The method includes the following steps. Measuring charging/discharging information of the battery. Calculating a charging/discharging characteristic of the battery according to the charging/discharging information. Aligning the charging/discharging characteristic of the battery according to a comparison characteristic point of a comparison characteristic to obtain an aligned charging/discharging characteristic. Determining whether the battery is normal according to the aligned charging/discharging characteristic or a coulombic efficiency of the battery; and when the battery is determined as abnormal, calculating aligned charging/discharging information according to the aligned charging/discharging characteristic, and calculating the resistance of the internal short circuit of the battery according to the aligned charging/discharging information.