Background: Acute kidney injury (AKI) after cardiovascular surgery (CVS) infers high morbidity and mortality and may be caused by thrombotic microangiopathy (TMA). This study aimed to assess incidence, risk factors, kidney function, and mortality of patients with a postoperative TMA as possible cause of severe AKI following cardiovascular surgery. Methods: We analyzed retrospectively all patients admitted to the ICU after a cardiovascular procedure between 01/2018 and 03/2019 with severe AKI and need for renal replacement therapy (RRT). TMA was defined as post-surgery-AKI including need for RRT, hemolytic anemia, and thrombocytopenia. TMA patients were compared to patients with AKI requiring RRT without TMA. Results: Out of 893 patients, 69 (7.7%) needed RRT within one week after surgery due to severe AKI. Among those, 15 (21.7%) fulfilled TMA criteria. Aortic surgery suggested an increased risk for TMA (9/15 (60.0%) vs. 7/54 (31.5%), OR 3.26, CI 1.0013-10.64). Ten TMA patients required plasmapheresis and/or eculizumab, and five recovered spontaneously. Preoperative kidney function was significantly better in TMA patients than in controls (eGFR 92 vs. 60.5 mL/min, p = 0.004). However, postoperative TMA resulted in a more pronounced GFR loss (ΔeGFR −54 vs. −17 mL/min, p = 0.062). There were no deaths in the TMA group. Conclusion: Our findings suggest TMA as an important differential diagnosis of severe AKI following cardiovascular surgery, which may be triggered by aortic surgery. Therefore, early diagnosis and timely treatment of TMA could reduce kidney damage and improve mortality of AKI following cardiovascular surgery, which should be further investigated.