A controller for an internal combustion engine that controls: a throttle valve that adjusts an intake air amount of air that is suctioned into the internal combustion engine; and a supercharger that drives a turbine by using exhaust gas that flows through an exhaust route of the internal combustion engine so as to supercharge the air that flows through an intake route into the internal combustion engine by a compressor coupled to the turbine, the controller for the internal combustion engine comprising: a target value setting section that sets a target intake air amount of the air that is suctioned into the internal combustion engine and target supercharging pressure of the air that is supercharged into the internal combustion engine based on an operation state of the internal combustion engine; a requested throttle valve opening degree computing section that computes a requested throttle valve opening degree that is requested to the throttle valve in accordance with the set target intake air amount; a requested exhaust flow rate adjusting valve opening degree computing section that computes a requested exhaust flow rate adjusting valve opening degree that is requested to an exhaust flow rate adjusting valve that adjusts a flow rate of the exhaust gas that flows through the exhaust route in accordance with the computed target supercharging pressure; and a filter processing section that executes filter processing in which a filter is applied to a variation in an instructed throttle valve opening degree that is instructed to the throttle valve so as to make the throttle valve follow the requested throttle valve opening degree, characterised in that the filter is a low pass filter with a variable pass characteristic based on time constants, and the pass characteristic based on time constants is set in accordance with the throttle valve opening degree deviation and the requested throttle valve opening degree, whereby the throttle valve opening degree deviation is equal to a difference between the requested throttle valve opening degree and the last instructed throttle valve opening degree that has been subjected to the filter processing, and the filter processing section extracts a filter with a pass characteristic that corresponds to the throttle valve opening degree deviation and the requested throttle valve opening degree and applies the extracted filter with the pass characteristic, so as to maintain or correct the variation in the instructed throttle valve opening degree that follows the requested throttle valve opening degree. a target value setting section that sets a target intake air amount of the air that is suctioned into the internal combustion engine and target supercharging pressure of the air that is supercharged into the internal combustion engine based on an operation state of the internal combustion engine; a requested throttle valve opening degree computing section that computes a requested throttle valve opening degree that is requested to the throttle valve in accordance with the set target intake air amount; a requested exhaust flow rate adjusting valve opening degree computing section that computes a requested exhaust flow rate adjusting valve opening degree that is requested to an exhaust flow rate adjusting valve that adjusts a flow rate of the exhaust gas that flows through the exhaust route in accordance with the computed target supercharging pressure; and a filter processing section that executes filter processing in which a filter is applied to a variation in an instructed throttle valve opening degree that is instructed to the throttle valve so as to make the throttle valve follow the requested throttle valve opening degree, characterised in that the filter is a low pass filter with a variable pass characteristic based on time constants, and the pass characteristic based on time constants is set in accordance with the throttle valve opening degree deviation and the requested throttle valve opening degree, whereby the throttle valve opening degree deviation is equal to a difference between the requested throttle valve opening degree and the last instructed throttle valve opening degree that has been subjected to the filter processing, and the filter processing section extracts a filter with a pass characteristic that corresponds to the throttle valve opening degree deviation and the requested throttle valve opening degree and applies the extracted filter with the pass characteristic, so as to maintain or correct the variation in the instructed throttle valve opening degree that follows the requested throttle valve opening degree.