Pyrolysis is considered as a promising method to immobilize potentially toxic elements (PTEs) in animal manures. However, comparative study on characteristics and environmental risk of PTEs in biochar obtained by pyrolysis of animal manure at different reactors are lacking. In this study, swine manure was pyrolyzed at 300–600 °C in a lab-scale or pilot-scale reactor with the aim to investigate their effects on characteristics and environmental risk of As, Cd, Cu, Ni, Pb, and Zn in swine manure biochar. Results showed that biochars produced from pilot scale had lower pH and carbon (C) content but higher oxygen (O) content than those from lab scale. Biochars from pilot scale had higher total PTEs (except Cd) concentrations and releasable PTEs (except Pb) but lower CaCl2-extractable PTEs and phytotoxicity germination index (GI) to radish seedings than those from lab scale. Chemical speciation analysis indicated that PTEs in biochar produced from pilot-scale fast pyrolysis at 400 °C had higher percentage of more stable fraction (F5 fraction) and lower potential ecological risk index (RI) than those from lab-scale slow pyrolysis. These findings demonstrated that bioavailability and potential ecological risk of PTE in swine manure biochar were greatly decrease in the pilot-scale pyrolysis reactor and the optimum temperature was 400 °C considering the lowest potential ecological risk index.