A motor drive system control apparatus includes: a direct current power supply; a three-phase alternating current motor; a first power converter including switching circuits corresponding to each of three phases of the three-phase alternating current motor and a smoothing condenser disposed electrically in parallel with the switching circuits; an estimating device for estimating peak generation timing in which a peak is generated in an inter-terminal voltage VH of the smoothing condenser on the basis of at least one of an operating condition of the three-phase alternating current motor; a switching condition of the switching circuits corresponding to each of the three phases; and a controlling device for controlling a drive condition of the first power converter so the inter-terminal voltage VH (or a VH peak) in the peak generation timing decreases, for a predetermined period from start timing set in a time domain before the estimated peak generation timing.