Objective To investigate the patterns and risk factors of central lymph node metastasis (CLNM) in the clinically node-negative neck (cN0) papillary thyroid microcarcinoma (PTMC) patients with tumor maximum diameter ≤ 5 mm. Methods A total of 186 patients with cN0 PTMC (tumor maximum diameter ≤ 5 mm) were enrolled from Department of General Surgery (Ⅲ), Changzheng Hospital, Second Military Medical University from Jan. 2011 to Dec. 2015. The clinicopathological characteristics of the patients were retrospectively analyzed, including gender, age, tumor location, bilateral carcinoma, multiplicity, extrathyroidal invasion, Hashimoto thyroiditis, and immunohistochemical results. χ² test and logistic regression were used to evaluate the patterns and risk factors of CLNM in cN0 PTMC patients. Results In this study, 58 (31.2%) of 186 patients with cN0 PTMC (tumor maximum diameter ≤ 5 mm) developed CLNM. The average number of lymph nodes in prophylactic lymph node dissection was 4.92±6.82 (ranged from 0 to 14), with the average number of metastatic lymph nodes being 0.78±1.41 (ranged from 0 to 5). The average ratio of metastatic lymph nodes number/dissected lymphatic nodes number was (50±28)% (ranged from 0% to 100%). Univariate analysis showed that gender and multifocal tumor were risk factors of CLNM (P<0.05). Multivariate analysis showed that male and multifocal tumor were independent risk factors of CLMM in PTMC (tumor maximum diameter ≤ 5 mm) patients (P<0.05). Conclusion Prophylactic central lymph node dissection may be more valuable for male cN0 PTMC (tumor maximum diameter ≤ 5 mm) patients with multifocal tumors.