Environmental research has widely utilized the ambient concentrations of hazardous air pollutants (HAPs) modeled by the National-Scale Air Toxics Assessment (NATA) program; however, limited studies have evaluated the model’s performance. This study aims to evaluate the model-to-monitor agreement of the 2011 NATA data with the monitoring data reported to the U.S. Environmental Protection Agency’s (EPA) Air Quality System (AQS). Concentrations of 27 representative HAPs measured at 274 sites in the U.S. in 2011 were merged with NATA data by census tract. The comparison consisted of two steps for each HAP: first, the model-monitor difference at each site was compared with the limit of quantitation (LOQ); second, the modeled annual average was compared to the 95% confidence interval of the monitored annual average. Nationally, NATA could predict national medians of most HAPs well; however, it was unable to capture high concentrations. At individual sites, a large portion of model-monitor differences was below the LOQs, indicating they were unquantifiable. Model-to-monitor agreement displayed inconsistent patterns in terms of chemical groups or EPA regions and was strongly impacted by the comparison methods. The substantial non-agreements of NATA predictions with monitoring data require caution in environmental epidemiology and justice studies that are based on NATA data.