Disclosed are a method and a system to control a low voltage DC converter for a vehicle, capable of realizing good dynamic performance of a vehicle by improving an engine cooling performance if a vehicle driving mode is a dynamic performance priority mode. The method to control a low voltage DC converter includes: a driving mode determining step of determining a driving mode of a vehicle; a priority confirming step of confirming a current control priority of a low voltage DC converter reducing high voltage power, supplied from a high voltage battery, to low voltage power if the driving mode is the dynamic performance priority mode; and an LDC control step of controlling an output voltage of the low voltage DC converter to make an input voltage of a vehicle engine cooling fan become a maximum value within a preset allowance if the current control priority, confirmed at the priority confirming step, is lower than a preset reference priority.
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