Pre-made carrots are fresh and ready to eat or to be cooked. However, processing steps such as washing, peeling, and slicing often result in juice loss and microbial contamination. In this study, an optimal combination between nisin and radio frequency (NRF) for synergistic processing of pre-made carrots was proposed by orthogonal tests. Pre-made carrots were separately treated by NRF, single nisin or radio frequency (RF), nisin and ultrasonic waves (NUW), or blanching, and then the total bacterial count, physiological quality, and physical microstructure during storage were compared between groups. The results showed that NRF treatment effectively inactivated bacteria (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) and extended the shelf life of pre-made carrots to 42 days. Carotenoids and ascorbic acid were considerably retained. The whiteness index and unacceptable odor of pre-made carrots were also significantly suppressed. Scanning electron microscopy (SEM) showed that the cellular microstructure of NRF-treated pre-made carrots had slight curling and folding, which was superior to NUW or blanching treatments. Pearson correlation analysis found that there were different correlations between the quality of pre-made carrots with different treatments. Therefore, the experimental results of this paper can provide help for food processing industry to produce high-quality pre-made carrots, and even other pre-made foods as well.