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Here we report a novel mass spectrometry measurement system (MSHE4) developed at State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences for quantifying helium-4 contents of geological mineral samples. The MSHE4 system consists of seven units, a high vacuum level generating unit, a gas purified unit, a laser heating unit, a pneumatic valve unit, an automatic control unit, a gas standard unit and a quadropole mass spectrometer unit. The unique software package, developed using LabVIEW for embedded system, allows users to control the full measurement sequences. Results from a test of the Durango apatite sample are used to illustrate the performance of the new MSHE4. We show that the constructed MSHE4 system is able to accurately measure helium-4 contents of apatite mineral, which in turn can be used to quantify the low temperature thermochronology of geological minerals in combination with measurements of uranium and thorium by LA-ICP-MS. The configuration of the MSHE4 system has following advantages: smaller volume of pipeline for gas purification, easier operation of graphic user interface for measurements, and more compact design of sample holder for single grain measurements. The separate step-heating unit can be mounted to the system smoothly. The MSHE4 system can be used for measurement of noble gases from minerals, and in turn thermochronology applications for geochemists.