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The gradient-based optimization methods are preferable for the large-scale three-dimensional (3D) magnetotelluric (MT) inverse problem. Compared with the popular nonlinear conjugate gradient (NLCG) method, however, the limited-memory Broyden–Fletcher–Goldfarb–Shanno (L-BFGS) method is less adopted. This paper aims to implement a L-BFGS-based inversion algorithm for the 3D MT problem. And we develop our code on top of the ModEM package, which is highly extensible and popular among the MT community. To accelerate the convergence speed, the preconditioning technique by the affine linear transformation of the original model parameters is used. Two modifications of the conventional L-BFGS algorithm are also made to get a comparable convergence rate with the NLCG method. The impacts of the preconditioner parameters, the regularization parameters, the starting model, etc., on the inversion are evaluated by synthetic examples for both L-BFGS and NLCG methods. And the real MT Kayabe dataset is also inverted by the inversion algorithms. The synthetic tests show that through our L-BFGS inversion algorithm the similar resistivity models can be obtained with that from the NLCG method. For the real data inversion, the L-BFGS method performs more efficiently and reasonable results could be obtained by less iterations of the inversion process than the NLCG method. Thus, we suggest the common usage of the L-BFGS method for the 3D MT inverse problem. [ABSTRACT FROM AUTHOR]