A mass spectrometer (MS) with nano-electrospray ionisation (nano-ESI) benefits the mass spectrometric analyses of samples of limited availability due to its low consumption of analyte with a micro-scale emitter. In a nano-ESI MS, a high voltage is applied to the emitter and the electric field introduces entrainment of ions into the atmosphere-vacuum interface of the MS. During this process, resistances from the buffer gas and the Coulomb repelling force lead to ion dispersion and the reduction of the ion transmission efficiency. Understanding of the ion transport behaviours in this process is essential to improve the device sensitivity. Numerical simulation of ion trajectories overcomes limited measurements in experiments to provide a full picture of ion transport properties and, furthermore, facilitates instrument design. However, the numerical simulation is still challenging due to the contradictory relationship between accuracy and computational cost in solving full governing equations of particle motions under combined gas dynamics and electric forces. In this numerical study, we developed user-defined functions (UDF) in ANSYS Fluent to simulate ion trajectories, taking account of a realistic space-charge effect in a continuous injection mode of nanospray in a cone-gas influenced ion source flow field.