A flow control baffle apparatus for a vehicle heater is provided. The flow control baffle apparatus implements a flow control function of a fluid passing through the interior of a heater and improves the heat transfer performance of the heater. The flow control baffle apparatus for a vehicle heater includes a plurality of heater pipes that are disposed within the interior of a heater and a baffle pivotably disposed at both sides of the heater pipe to adjust the flow of a fluid. Wherein the baffle adjusts the flow rate of a fluid passing through the heater.