High-dose chemotherapy followed by autologous stem cell transplantation (ASCT) has become the standard salvage treatment for primary high-risk and relapsed/refractory lymphoma patients. The conditioning regimen has evolved from one that included total body irradiation (TBI) to one that includes high-dose chemotherapy, as well as combinations of novel drugs. We systematically reviewed existing research data and summarize the survival benefits, treatment-related adverse events, and hematopoietic reconstitution after various conditioning regimens. As a classical conditioning regimen, BEAM (carmustine, etoposide, cytarabine, and melphalan) can eliminate minimal residual disease and achieve long-term disease-free survival. However, considering the safety, tolerability, and accessibility of these drugs, it still needs to be improved. In recent years, with the continuous development of novel drugs, new combinations have emerged. An efficient and low toxicity regimen is crucial for the survival benefits of patients undergoing ASCT. Alternative regimens such as GBC (gemcitabine, busulfan, and cyclophosphamide)/GBM (gemcitabine, busulfan, and melphalan), BeEAM (bendamustine, etoposide, cytarabine, and melphalan), and SEAM (semustine, etoposide, cytarabine, and melphalan) are safe and feasible. Data from studies combining these regimens with novel drugs are even more attractive. Ultimately, future conditioning regimens will show low toxicity, be highly efficient, and be personalizable with respect to lymphoma subtype and comorbidities.