A charged particle beam writing apparatus includes a writer writing a pattern on a surface of a substrate using a charged particle beam, a measurement unit measuring a height of the surface of a central portion of the substrate at a plurality of positions in the central portion, a generator performing fitting using a first polynomial on measurement values from the measurement unit, calculating, by extrapolation using the first polynomial, a first height distribution of the height of the surface of a peripheral portion of the substrate, performing fitting using a second polynomial, which is of a higher order than the first polynomial, on the measurement values, calculating a second height distribution of the height of the surface of the central portion by interpolation using the second polynomial, and generating a height distribution of the substrate by combining the first height distribution and the second height distribution, and a controller adjusting a focal position of the charged particle beam based on the height of the surface at a writing position, the height being calculated from the height distribution of the substrate.