The study examined the diagnostic value of low-flow and low-dose DECT (dual energy CT) in combination with D-dimer and mMRC scores in the evaluation of lung lesions in 92 patients with post-COVID-19 syndrome after Omicron infection. The positive group had a significantly higher median age and median D-dimer value than the negative group. A higher mMRC score was associated with a greater likelihood of abnormal D-dimer values, with no positive case exceeding mMRC grade 3 and no severe clinical signs. Interobserver agreement for DECT parameters was excellent (ICC 0.8–1.0). DECT perfusion revealed a significantly larger volume of abnormally perfused lung tissue and a lower mean iodine density in these areas in the positive group (P < 0.001). The combined diagnostic model achieved an AUC of 0.969, which significantly outperformed the individual parameters (P < 0.001). The low flow and low dose of DECT increases patient safety and accurately identifies functional lung abnormalities invisible to conventional CT or CTPA. Combined with clinical data, it significantly improves the diagnostic accuracy for post-COVID-19 syndrome.