Appropriate analytical methods are required to evaluate the presence, metabolism, degradation, and removal of specific compounds in complex mixtures. There is an increasing demand to analyze samples with a wide range of polarities in a variety of applications, including environmental analysis, biomarker discovery, and proteomics. Multiple analyses on complementary columns are often needed to cover the separation of all compounds with a large difference in polarity. This article describes a generic method involving an ultrahigh-pressure liquid chromatography (UHPLC) system equipped with two external switching valves to connect hydrophilic interaction liquid chromatography (HILIC) and reversed-phase LC columns in series for the sequential analysis of polar and apolar compounds. The method was successfully applied to separate 32 pharmaceutical compounds with a wide range of polarities, which could be useful for analyzing pharmaceutical compounds in the environment.