The incident beam quality at the target determines the resolution and intensity of micro-focus X-ray sources, which depends greatly on the focusing system and the target. To meet different spatial layouts of the focusing system with transmission and reflection targets, three-dimension (3-D) modelling of the focusing system was built with Monte Carlo simulation and coordinate transforming method in this paper. In the proposed approach, the focusing system was first optimized by a 2-D model to achieve a fine beam spot with high effective current at the optimum working distance for the transmission and reflection targets. Then, 3-D practical model of the focusing system was achieved by tracing N electrons from the electron gun in three directions using the 5-order Runge-Kutta method. Finally, examples of the focusing system for 90 keV and 30 keV X-ray sources were given to get the energy distributions at transmission and reflection targets. Results show that resolutions of 4 μm and 500 nm have been achieved for 90 keV X-ray source with the transmission target and 30 keV X-ray source with the reflection target respectively. Compared with the experimental results, 2-D modelling of the focusing system is also applicable for X-ray source with the transmission target while 3-D modelling of the focusing system is essential for X-ray source with the reflection target. In addition, the 3-D electron beam model will simplify the design of the real apertures, liner tubes, beam blankers etc.