In order to study the influence of the structure of high fill loess on its strength and deformation characteristics under unconfined compression, taking the loess of a high fill site in Yan’an New Area as the research object, we carried out a series of unconfined compressive strength tests of undisturbed loess and remolded loess under different test conditions. We investigated the influence of water content and compactness on the change law and mechanical properties of the loess structure, and then established a mathematical model that can reflect the interplay between the initial structural parameters and compressive strength of undisturbed loess and remodeled loess. The findings show that with the increase of water content or the decrease of compactness, the stress-strain curve of the loess changes from “steep” to “stable”, the peak characteristic strength decreases and moves back towards the end of the curve; however, the peak point of structural parameter strain curve decreases and moves forward. The plasticity index can be used as a critical value indicator that affects the initial structural parameter change, when the water content is less than the value of plastic limit, a small strain can lead to structural enhancement and vice versa. With the increase of water content, the initial structural parameter decreases non-linearly but the compressive strength decreases linearly. The distribution of structural parameter strain curve of the undisturbed loess is more “steep” than that of the remolded loess, and the initial structural weakening capacity of the undisturbed loess is significantly greater than that of the remolded loess with increased humidity. There is a good non-linear relationship between initial structural parameters and compressive strength of the undisturbed loess and remolded loess, which can be characterized by a hyperbolic function model based on compressive strength, saturated loess compressive strength and initial structural parameters.