<p>Three-dimensional (3-D) magnetotelluric (MT) inversion outcomes are influenced by various user-defined configurations, yet comprehensive analyses and rigorous testing of them are rarely conducted, particularly for 3-D large-scale surveys. Additionally, different inversion frameworks will inevitably yield varying “preferred” models, highlighting the need to investigate the reasons behind these discrepancies, which can uncover model uncertainties linked to algorithm-specific choices. This study focuses on analyzing and comparing factors from the above two categories that contribute to uncertainties in inversions and interpretations. First, to explore the user-defined configurations that lead to differing results, we performed multiple tests using the USArray MT data. Specifically, we assessed the impact of regularization parameters, prior information, projection methods, regularization types, data types and frequencies, initial models, mesh settings, and distortion correction on inversion outcomes by the two most widely used inversion frameworks: ModEM and FEMTIC. After thoroughly analyzing these factors, we present a new electrical model for the Northwestern U.S.&#xa0;using FEMTIC code. The primary conductivity variation of this model aligns well with a previous one obtained by utilizing ModEM. However, large-scale differences between the two “preferred” solutions are still observed. We conclude that the discrepancies in geologically active high-conductivity zones are mainly due to different selection method for regularization parameter and mesh settings, and difference in average resistivities of the lower upper mantle primarily stem from differing degrees of dependence on the initial model, a distinction that fundamentally stems from differences in regularization assumptions and optimization algorithms.</p>