Eddy current sensors can be used to test the characteristics and measure the parameters of the conductive samples. As the main obstacle of the multi-frequency eddy current sensor, the lift-off distance affects the effectiveness and accuracy of the measurement. In this paper, a material-independent algorithm has been proposed for the restoration of the lift-off distance when using the multi-frequency eddy current sensor, which is based on the approximation under the thin-skin effect. Experiment testing on the performance of the proposed method is presented. Results show that from the dual-frequency inductance, the lift-off distance could be restored with a maximum error of 0.24 mm for the distance up to 12 mm. Besides, the derived lift-off distance is used for the inversion of the magnetic permeability. Based on a lift-off insensitive inductance (LII) feature, the magnetic permeability of steels can be inversed in an iterative manner, with an error of less than 0.6 % for the lift-off distance up to 12 mm.