We examined the degree of calculated-to-measured dose difference for nasopharyngeal target volume in intensity-modulated radiotherapy (IMRT) based on the observed/expected ratio using patient anatomy with humanoid head-and-neck phantom. The plans were designed with a clinical treatment planning system that uses a measurement-based pencil beam dose-calculation algorithm. Two kinds of IMRT plans, which give a direct indication of the error introduced in routine treatment planning, were categorized and evaluated. The experimental results show that when the beams pass through the oral cavity in anthropomorphic head-and-neck phantom, the average dose difference becomes significant, revealing about 10% dose difference to prescribed dose at isocenter. To investigate both the physical reasons of the dose discrepancy and the inhomogeneity effect, we performed the 10 cases of IMRT quality assurance (QA) with plastic and humanoid phantoms. Our result suggests that the transient electronic disequilibrium with the increased lateral electron range may cause the inaccuracy of dose calculation algorithm, and the effectiveness of the inhomogeneity corrections used in IMRT plans should be evaluated to ensure meaningful quality assurance and delivery.