Different treatments of autoclaving, pullulanase debranching and/or ultrasound were applied to prepare debranched lentil starch (DBLS). Their fine structures can affect the retrogradation patterns of DBLSs, which consequently could affect their potential use as delivery carrier of sensitive bioactive compounds. An attempt was made to use these DBLSs as wall materials to encapsulate rutin, aiming to improve the bioaccessibility, meanwhile to enhance the aqueous solubility and stability of rutin molecules. Their encapsulation efficiency, structural characteristics, thermal stability, morphological features, antioxidant activity and in vitro release behavior under simulated upper gastrointestinal tract environment were evaluated. The results suggested that rutin was dispersed in the DBLS polymer matrix, showing the amorphous nature that further authenticates the encapsulation and entrapment of rutin. The structural analyses of microparticles revealed that rutin could interacted with DBLS biopolymer chains by hydrogen bonds, making the starch molecular chains less susceptible to interact with themselves for reordering. The encapsulation efficiency was found to be in an opposite trend with those values obtained for relative crystallinity, melting enthalpy, degree of order/double helices of DBLS wall materials before encapsulation. The release rate results indicated that DBLS carrier with lower Mw, DPn and higher molecular order was beneficial for the slower release of rutin encapsulated in the microparticles.