Background and Aims Many previous studies comparing liver resection versus thermal ablation for colorectal cancer liver metastases (CRCLM) are subject to severe selection bias. This study aimed to compare the long-term clinical efficacy of ultrasonography-guided percutaneous microwave ablation (PMWA) with resection for CRCLM using propensity score analysis to reduce confounding by indication. Methods This retrospective study included 184 patients with CRCLM from January 2012 to June 2017. Treatment effect was estimated after propensity score matching, Descriptive, regression and survival statistics were applied. Results A lower American Society of Anesthesiologists classification score and higher performance status were found positively associated with resection (p < 0.05). After propensity score matching, the 1-, 2-, and 3-year local tumor progression free survival rates were found to be 60.3%, 19.1%, and 17.6% in the PMWA group, and 72.1%, 35.3%, 26.5% in the resection group, respectively (p = 0.049). The 1-, 3-, 5-, and 7-year overall survival rates in two groups were similar (p = 0.943). In the PMWA group and resection group, the median hospital stay was 1 (0-12) days and 7 (1-27) days (p = 0.005), respectively; major complications occurred in two patients (2%) and 11 patients (12.9%) (p = 0.009), respectively. Conclusions After adjusting for factors known to affect treatment choice, no significant difference in overall survival rates was shown after ultrasound-guided PMWA versus resection for CRCLM. The LTPFS rate of the resection group were better than those of the ultrasound-guided PMWA group. However, the ultrasound-guided PMWA group had fewer complications and shorter hospital stay.