Due to challenges in diagnosis and the need for complex laboratory tests, misdiagnosis of neurosyphilis and tertiary syphilis is common in China. We validated the diagnosis and examined the treatment of late neurosyphilis and tertiary syphilis in Guangdong Province, China. A cross-sectional study was conducted to collect data from late neurosyphilis and tertiary syphilis cases reported between 2009 and 2014 in Guangdong, China. Descriptive analysis, bivariate analyses and multiple logistic regressions were performed to determine the structural factors associated with correct diagnosis and standard treatment of late neurosyphilis and tertiary syphilis. Among the 3805 respondents (3805/3936, 96.7%), 1,837 (48.3%) met the misdiagnosed criteria. The misdiagnosis rate decreased over the study period (54.2% in 2009 and 41.8% in 2014). Only 27.1% and 24.9% of the correctly diagnosed late neurosyphilis and tertiary syphilis cases received standard treatment, respectively. Multiple logistic regression revealed that departments of dermatology or STDs [aOR = 3.24, 95% CI: 2.66-3.95], county or township level hospitals [aOR = 2.89, 95% CI: 2.14-3.89], and hospitals situated outside of Pearl River Delta area [aOR = 1.70, 95% CI: 1.46-1.97] had higher likelihood in misdiagnosis of neurosyphilis, compared to the reference groups. Targeted trainings for physicians and expanded syphilis screening services are urgently needed.