Objective To analyze and compare the diagnostic value of two modes of photonic dual source CT pulmonary angiography. Methods A total of 80 cases of male patients with suspected pulmonary embolism who were treated in our hospital between May 2011 and July 2015 were selected and were randomized into group A and B. Group A underwent dual energy pulmonary angiography while group B underwent Flash mode imaging. Iterative reconstruction algorithm was used for image reconstruction. The CT values, noise (SD), signal to noise ratio (SNR), contrast noise ratio (CNR) and CT dose index volume (CTDIvol), effective dose length product (DLP) and effective radiation dose (ED) were compared between the two groups. Results The CT value of image of patients in group A (364.2±63.7) Hu was significantly higher than that in group B (643.5±91.4) Hu while SD (20.4±3.9) Hu was significantly lower than that in group B (37.1±4.6) Hu (P<0.05). There were no significant differences in SNR and CNR values between different ROI in the two groups (P>0.05). The CTDIvol, DLP and ED of group B was significantly less than that of group A [(1.67±0.32) mGy, (54.24±5.91) mGym.cm, (0.63±0.09) mSvT VS (8.43±1.06) mGy, (250.41±51.60) mGym·cm, (3.27±0.62) mSvT] (P<0.05). Conclusion The comparison of dual source CT Flash mode combined with iterative reconstruction technique and dual energy scan mode not only can meet the requirement of image diagnosis, but also can reduce the radiation dose.