Backgrounds: Transferring behaviors of a human’s upper-limbs to an avatar is widely used in the field of virtual reality rehabilitation. To realize the transfer, movement tracking technology is required. Traditionally, wearable tracking devices are used to do the tracking, however the devices are expensive and cumbersome. Recently, non-wearable upper-limb tracking solutions are proposed, which are cheaper and more comfortable to interact. But most of the existing products cannot track full upper-limbs including both the arms and all the fingers, which limits the motion paradigm and further may lead to limited rehabilitation effect. Methods: In this paper, a novel method was first proposed for full avatar’s upper-limb control which integrates the fine finger motion and the arm wide range motion. Then, based on the method, a Virtual Reality Rehabilitation System (VRRS) was developed for upper-limb rehabilitation. To test the performance of VRRS, two experiments were designed. First, in order to investigate the effect of VRRS on virtual body ownership, agency, location of the body and usability, we compared it with the partial upper-limb tracking method based on Leap Motion controller (LP) in same virtual environments. Then, to study the feasibility of VRRS in rehabilitation, we recruited 16 stroke patients and split them into two groups: the experimental group and the control group. Each group consisted 8 patients, with and without employing VRRS respectively.Results: The control of full avatar’s upper-limbs improved the users’ senses on body ownership, agency and location of the body. The users preferred to use VRRS. In addition, although the upper-limb motor function of patients from both groups were improved, the difference between the FM scores tested on the first day and the last day of the experimental group was more significant than that of the control group. Conclusions: VRRS based on the proposed method for full avatar’s upper-limbs control was developed, which improved the user experience on embodiment and effectively improved the rehabilitation effect for upper-limbs of stroke patients.Trial registration:The study was registered at the First Affiliated Hospital of Jinan University Identifier: KY-2020-036; Date of registration - June 01, 2020.