A heat dissipation system includes a motherboard, at least two chips, at least two heat sinks and at least two air guide covers. Every two chips of the at least two chips constitute a chipset, the chips in each chipset are installed on the motherboard in sequence along an airflow direction, each of the at least heat sinks is installed on a surface of the chip corresponding to the heat sink, and every two air guide covers of the at least two air guide covers constitute an air guide group. In the air guide group, a first air guide cover is arranged on a first side of a first chip, and a second air guide cover is arranged on a second side of a second chip. A heat dissipation method based on the system is also provided. The solution ensures a relatively uniform heat dissipation between the chips.