In this paper, a least-squares spectral method and a non-conforming least-squares spectral element method for three dimensional linear elliptic system will be presented. Differentiability estimates and the main stability theorem for the proposed method are proven. Using the regularity estimate and the proposed stability estimates, we introduce a suitable preconditioner and show that the condition number of the preconditioned system is O((ln W) 2) (where W is degree of polynomials). Then we establish the error estimates of the proposed method. Specific numerical results based on linear elasticity problem, fourth order problem and sixth order problem are discussed to reflect the efficiency of the proposed method. Keywords Least-squares methods • Non-conforming methods • Spectral element method • Linear elliptic system in three dimensional space • Fourth order problems • Sixth order problem • Linear elasticity problem • Preconditioner • Exponential accuracy Dedicated to Professor Chandra Shekhar Upadhyay on the occasion of his 50th birthday Research is supported by EPSRC Grant EP/P013317/1.