The study of secondary particles produced by the cosmic-ray interaction in the Earth’s atmosphere is very crucial as these particles mainly constitute the background counts produced in the high-energy detectors at balloon and satellite altitudes. In the present work, we calculate the abundance of cosmic-ray generated secondary particles at various heights of the atmosphere by means of a Monte Carlo simulation and use this result to understand the background counts in our X-ray observations using balloon-borne instruments operating near the tropical latitude (geomagnetic latitude: ~14.50°N). For this purpose, we consider a 3D description of the atmospheric and geomagnetic field configurations surrounding the Earth, as well as the electromagnetic and nuclear interaction processes using Geant4 simulation toolkit. Subsequently, we use a realistic mass model description of the detector under consideration, to simulate the counts produced in the detector due to secondary cosmic-ray particles.