Herein, we describe a practical online supercritical fluid extraction-supercritical fluid chromatography/mass spectrometry (SFE-SFC/MS) system with an integrated split-flow method and a pre-column trap method that is well suited for the continuous extraction and separation of a wide range of compounds, including hydrophilic ones. Although an SFE-SFC system with a splitting method is already commercially available, in this study, we added some new features to this system: 1) a splitting method that further reduces the amount of extractant introduced into SFC, 2) a trap column, connected before the analytical column, with a different separation mechanism than the analytical column in the system with the splitting method, and 3) a system for calculating the recovery rate of SFE during online SFE-SFC/MS. In the above setup, part of the analyzed extract is introduced into the separation section at a higher split ratio owing to the make-up pump flow rate, thus reducing the distortion of the target analyte peak shape caused by the use of a strong extractant. Furthermore, the separation efficiency is improved by the use of an additional pre-column capable of interacting with compounds weakly retained on the analytical column. Finally, we show that equalization of the SFE and autosampler injection conditions allows evaluation of the recovery rate of SFE during online SFE-SFC/MS.