Neoclassical properties in quasi-axisymmetric (QA) stellarators are analogous to these in tokamaks. Consequently, a substantial bootstrap current could significantly modify the MHD equilibrium properties of a QA stellarator, which is an important characteristic in this type of stellarator. This paper is dedicated to systemically investigate the effects of bootstrap current on the magnetic configuration in Chinese First Quasi-axisymmetric Stellarator (CFQS). For the first time, self-consistent bootstrap currents in free-boundary equilibria are calculated with an accurate Fokker–Planck neoclassical numerical mode in CFQS. Several important results are achieved: 1) As the bootstrap current grows with increasing volume-averaged normalized pressure β, the magnetic shear develops in the bulk plasma and meanwhile, a deep magnetic well is robustly sustained, which leads to improved stabilization of interchange modes up to β~2.0%. 2) In the analysis of global ideal MHD instability, as the bootstrap current rises to 39kA (β~1.3%), external kink modes become destabilized and the unstable mode with m/n= 2/1 is dominant. 3) From β=0 to 1.5%, the bootstrap current hardly changes the quasi-axisymmetric property and a low neoclassical transport is maintained. However, as β is enhanced beyond 2.0%, the substantial bootstrap current gives rise to an increase of non-quasi-axisymmetric magnetic field components, which weakens the neoclassical transport properties. 4) An increase of the negative magnetic shear at the core region by the bootstrap currents has a favorable effect on the properties of J (second adiabatic invariant). The maximum-J region can be extended by raising bootstrap currents.