Objective: This study aimed to explore the best thawing method for beetroots in freeze-thaw pretreatment. Methods: The frozen beetroots were thawed using different thawing methods （room temperature thawing, running water thawing, refrigeration thawing, microwave thawing, and ultrasonic thawing）, and then the thawed beetroots were subjected to microwave drying. The effects of different thawing methods on the microwave drying time, rehydration ratio, color, betalains content, total phenolic content, and total flavonoids content of microwave-dried beetroots were evaluated. Results: The results showed that refrigeration thawing required the longest thawing time, but the thawing loss rate was the smallest and the rehydration ratio of microwave-dried beetroots was the largest, which was 4.82. Meanwhile, running water thawing could better maintain the color of microwave-dried beetroots. There was no significant difference in microwave drying time among different thawing methods. It was found that the microwave-dried beetroots prepared by ultrasonic thawing showed the highest betacyanins content, and the microwave-dried beetroots obtained by microwave thawing displayed the highest betaxanthins content. Compared with other thawing methods, running water thawing resulted in higher total phenolic content and total flavonoids content of microwave-dried beetroots, which was 8.15 mg GAE/g and 16.50 mg RE/g, respectively. Conclusion: Running water thawing was a more suitable method for the thawing of frozen beetroots, which could provide better physicochemical properties of microwave-dried beetroots.