The invention brings forward a mass spectrum apparatus capable of detecting neutral molecule products and ion products, and an operating method thereof. The mass spectrum apparatus comprises a quandrupole rod series-connection special linear ion trap mass analyzer, a reagent molecule introduction ion trap accurate control system, a cushion gas flow introduction accurate control system, a vacuum gauge, a multistage gradient vacuum system, an electric control vacuum isolating valve system, an electron bombardment source mass spectrum system, and other necessary parts. The invention also provides a method of operating the above apparatus to carry out a molecule and ion reaction, accurately measure ion products of a molecule and ion reaction, extracting neutral molecules from products, ionize neutral molecules and then analyze ions.