An apparatus for controlling a converter of an eco-friendly vehicle includes: a high-voltage battery; a low-voltage conversion converter configured to convert power supplied from the high-voltage battery into a low voltage to provide power to at least one of an auxiliary battery of the vehicle and an electric load thereof; a renewable energy generator configured to generate power using renewable energy including solar light; a renewable energy conversion converter configured to convert the power supplied from the renewable energy generator to provide power to the at least one of the auxiliary battery and the electric load; and a controller configured to control an output voltage value of the low-voltage conversion converter and an output current of the renewable energy conversion converter.