A high-efficient algorithm to solve Crank-Nicolson scheme for variable coefficient parabolic problems is studied in this paper, which consists of the Function Time-Extrapolation Algorithm (FTEA) and Matrix Time-Extrapolation Algorithm (MTEA). First, FTEA takes a linear combination of previous l level solutions as good initial value of Un(see Time-extrapolation algorithm (TEA) for linear parabolic problems, J. Comput. Math., 32(2) (2014), pp. 183–194), so that Conjugate Gradient (CG)-iteration counts decrease to 1/3~1/4 of direct CG. Second, MTEA uses a linear combination of exact matrix values in level L, L+s, L+2s to predict matrix values in the following s–1 levels, and the coefficients of the linear combination is deduced by the quadric interpolation formula, then fully recalculate the matrix values at time level L+3s, and continue like this iteratively. Therefore, the number of computing the full matrix decreases by a factor 1/s. Last, the MTEA is analyzed in detail and the effectiveness of new method is verified by numerical experiments.