Numerical simulation is conducted using pure water as medium to investigate the flow distribution and convective heat transfer characteristic in parallel mini-channel heat sink. The effect of inlet and outlet arrangements, header structure and aspect ratio of channel on flow distribution and heat transfer are analyzed. The results showed that the flow uniformity of heat sink with I-type and rectangular header structure is better than other structures, and has the minimum standard deviation of mass flow rate (SI=0.071). For the same hydraulic diameter, the aspect ratio of channel has a little effect on average temperature of heat surface, whereas it has a significant effect on heat transfer coefficient, and the convective heat transfer coefficient improve 23.9% when the aspect ratio changed from 1 to 5. Base on field synergy principle, the synergy angle between the velocity and temperature field decrease with the increasing of aspect ratio, it suggest that heat transfer is enhanced.