BackgroundPhoton‐counting computed tomography (PCCT) has recently emerged into clinical use; however, its optimum imaging protocols and added benefits remains unknown in terms of providing more accurate lung density quantification compared to energy‐integrating computed tomography (EICT) scanners.PurposeTo systematically assess the performance of a clinical PCCT scanner for lung density quantifications and compare it against EICT.MethodsThis cross‐sectional study involved a retrospective analysis of subjects scanned (August‐December 2021) using a clinical PCCT system. The influence of altering reconstruction parameters was studied (reconstruction kernel, pixel size, slice thickness). A virtual CT dataset of anthropomorphic virtual subjects was acquired to demonstrate the correspondence of findings to clinical dataset, and to perform systematic imaging experiments, not possible using human subjects. The virtual subjects were imaged using a validated, scanner‐specific CT simulator of a PCCT and two EICT (defined as EICT A and B) scanners. The images were evaluated using mean absolute error (MAE) of lung and emphysema density against their corresponding ground truth.ResultsClinical and virtual PCCT datasets showed similar trends, with sharper kernels and smaller voxel sizes increasing percentage of low‐attenuation areas below ‐950 HU (LAA‐950) by up to 15.7 ± 6.9% and 11.8 ± 5.5%, respectively. Under the conditions studied, higher doses, thinner slices, smaller pixel sizes, iterative reconstructions, and quantitative kernels with medium sharpness resulted in lower lung MAE values. While using these settings for PCCT, changes in the dose level (13 to 1.3 mGy), slice thickness (0.4 to 1.5 mm), pixel size (0.49 to 0.98 mm), reconstruction technique (70 keV‐VMI to wFBP), and kernel (Qr48 to Qr60) increased lung MAE by 15.3 ± 2.0, 1.4 ± 0.6, 2.2 ± 0.3, 4.2 ± 0.8, and 9.1 ± 1.6 HU, respectively. At the optimum settings identified per scanner, PCCT images exhibited lower lung and emphysema MAE than those of EICT scanners (by 2.6 ± 1.0 and 9.6 ± 3.4 HU, compared to EICT A, and by 4.8 ± 0.8 and 7.4 ± 2.3 HU, compared to EICT B). The accuracy of lung density measurements was correlated with subjects’ mean lung density (p < 0.05), measured by PCCT at optimum setting under the conditions studied.ConclusionPhoton‐counting CT demonstrated superior performance in density quantifications, with its influences of imaging parameters in line with energy‐integrating CT scanners. The technology offers improvement in lung quantifications, thus demonstrating potential toward more objective assessment of respiratory conditions.