Breast reconstruction consists primarily of two methods: autologous breast reconstruction (ABR) and implant-based breast reconstruction (IBR). Each of these methods has its advantages and disadvantages. The current study used the National Inpatient Sample (NIS), the largest inpatient database in the United States, to explore the trends, complications, and disparities in the use of IBR and ABR. The current study used the NIS database from 2016 to 2020, including the International Classification of Diseases, 10th version (ICD-10) codes. A propensity score-matching (1:1) analysis was used to match the IBR and ABR groups. The percentage of breast reconstruction increased from 58.8% in 2016 to 63.4% by 2020. The trend of ABR was upward, and the trend of IBR was downward. In addition, the ABR group had significantly higher rates of cardiovascular complications (odds ratio [OR], 1.29), respiratory complications (OR, 4.26), vascular complications requiring surgery (OR, 7.82), blood transfusions (OR, 3.44), vasopressor need (OR, 1.409), and acute kidney injury (OR, 1.68). However, the ABR group had significantly lower rates of wound infection (OR, 0.430), wound dehiscence (OR, 0.213), wound seroma (OR, 0.602), and sepsis (OR, 0.252). A significant disparity was found in using ABR for different subgroups based on age, hospital teaching status, racial background, socioeconomic status, and hospital bed size. The current study showed an upward trend in the utilization of ABR and a downward trend for IBR. Although ABR had a higher rate of pulmonary, cardiovascular, vascular, and bleeding complications, it had a lower rate of wound-related complications.