Previous studies reported that the degree of hypoxemia following acute pulmonary thromboembolism (APTE) was highly variable and that its mechanism was mainly due to the creation of many high and low ventilation/perfusion (V/Q) units, as a result of the heterogeneous regional blood flow (Q) caused by embolic obstruction. We studied the effect of changing cardiac output (Qt) on gas exchange after APTE in 5 embolized piglets (23 ± 3 Kg), using Dobutamine intermittently at approximately 20 μg/kg/min for 120 minutes. The distribution of ventilation (V) and perfusion (Q) at various times was mapped using fluorescent microspheres in 941 ± 60 lung regions. After APTE, increase in Qt by Dobutamine improved venous oxygen tension (PvO2) but arterial PaO2 did not change consistently. On the other hand, cluster analysis showed that the V/Q ratio of most lung regions was lowered due to increases in Q at the same time. We concluded that the effect of changing cardiac output on gas exchange following APTE was affected by the simultaneous and varying balance between the changing V/Q mismatch and the concomitantly changing PvO2, which might explain the unpredictability of PaO2 in the clinical setting.