Currently the surgical approach for papillary thyroid microcarcinoma (PTMC), particularly the range of lymph node dissection, remains controversial. The present study aims to evaluate the risk factors for central and lateral lymph node metastasis (CLNM and LLNM) for appropriate clinical decision of neck lymph node dissection in PTMC. A total of 66 cases of PTMC that underwent unilateral or bilateral lobectomy plus prophylactic cervical lymph node dissection were collected for clinicopathological evaluation, including age, gender, tumor size, subtypes, extrathyroidal invasion, multifocality, calcifications, loss of cellular polarity/cohesiveness (LOP/C) in the invasive front, CLNM and LLNM, and retrospectively analysis. Univariate analysis revealed that LOP/C was significantly associated with CLNM (P=0.001) and LLNM (P<0.0001). The male gender was a risk factor of CLNM (P=0.04), while the age <45 years, tumor size >0.5 cm and multifocality were high-risk factors of LLNM (P=0.022, 0.044 and 0.005, respectively). Multivariable analysis revealed that LOP/C was significantly associated with CLNM [P=0.007, odds ratio (OR)=7.765, 95% confidence interval (CI)=1.773–33.996] and LLNM [P=0.029, OR=5.717, 95% CI=1.190–27.470]. Both multivariable analysis and χ2 test revealed that CLNM was another important high-risk factor of LLNM (P=0.021, OR=5.444, 95% CI=1.290–22.969, χ2=17.867, P<0.001). The present study revealed that prophylactic central lymph node dissection is essential for PTMC surgery and that prophylactic lateral lymph node dissection is recommend for patients with LOP/C and CLNM, which can be performed by intraoperative frozen section pathological examination. This must be considered discreetly in the case of patients with age <45 years, tumor size >0.5 cm and multifocal lesions.