Aim: To assess the ablative margin (AM) after microwave ablation (MWA) for hepatocellular carcinoma (HCC) with a deep learning-based deformable image registration (DIR) technique and analyze the relation between the AM and local tumor progression (LTP). Patients and Methods: From November 2012 to April 2019, 141 consecutive patients with single HCC (diameter ≤ 5 cm) who underwent MWA were reviewed. Baseline characteristics were collected to identify the risk factors for the determination of LTP after MWA. Contrast-enhanced magnetic resonance imaging scans were performed within 1 month before and 3 months after treatment. Complete ablation was confirmed for all lesions. The AM was measured based on the margin size between the tumor region and the deformed ablative region. To correct the misalignment, DIR between images before and after ablation was achieved by an unsupervised landmark-constrained convolutional neural network. The patients were classified into two groups according to their AMs: group A (AM ≤ 5 mm) and group B (AM > 5 mm). The cumulative LTP rates were compared between the two groups using Kaplan-Meier curves and the log-rank test. Multivariate analyses were performed on clinicopathological variables to identify factors affecting LTP. Results: After a median follow-up period of 28.9 months, LTP was found in 19 patients. The mean tumor and ablation zone sizes were 2.3 ± 0.9 cm and 3.8 ± 1.2 cm, respectively. The mean minimum ablation margin was 3.4 ± 0.7 mm (range, 0-16 mm). The DIR technique had higher AUC for 2-year LTP without a significant difference compared with the registration assessment without DL (P = 0.325). The 6-, 12-, and 24month LTP rates were 9.9, 20.6, and 24.8%, respectively, in group A, and 4.0, 8.4, and 8.4%, respectively, in group B. There were significant differences between the two groups (P = 0.011). Multivariate analysis showed that being >65 years of age (P = 0.032, hazard ratio (HR): 2.463, 95% confidence interval (CI), 1.028-6.152) and AM ≤ 5 mm (P = 0.010, HR: 3.195, 95% CI, 1.324-7.752) were independent risk factors for LTP after MWA. An et al. Using Deep Learning for Registration Conclusion: The novel technology of unsupervised landmark-constrained convolutional neural network-based DIR is feasible and useful in evaluating the ablative effect of MWA for HCC.