The present disclosure provides a system and method for retrieving temperature information of GPUs of a server system via PCIe topology, and using a baseboard management controller (BMC) to control fan speed(s) of cooling fans based at least upon the temperatures of the GPUs. In some implementations, the management controller can determine a PCIe topology of the server system via an operating system (OS), and get the BusID of each GPU or GPU card of the server system. Based upon the BusID, the management controller can retrieve temperature information of a corresponding GPU from a GPU library (e.g., NVIDIA Management Library [NVML]), and further control fan speed of cooling fan(s) based at least upon the temperature information.