In this paper, an acousto-optic tunable flat top filter is proposed by using one-dimensional coupled-cavity photonic crystal, and two kinds of materials, i.e. magnesium fluoride and tellurium dioxide, are selected. Based on the theory of acousto-optic effect, the thickness and refractive index of one-dimensional coupled cavity photonic crystal acousto-optic medium are changed by varying the ultrasonic frequency. After the parameters of acousto-optic medium are changed, the central wavelength of flat top filter of transmission spectrum shifts toward the short wave direction, thus realizing tunable filtering function. Based on the transfer matrix method and the theory of acousto-optic effect, the theoretical model of the flat top filter is established. The rectangularity, passband bandwidth, insertion loss and tunability of flat top filter are simulated by COMSOL software. The results show that the tuning effect can be achieved by applying a certain frequency of ultrasound in the case of different ultrasonic amplitudes. The decreasing trends of transmittance are basically identical in the process of changing ultrasonic frequency in the case of different amplitudes. When the central wavelength of the flat top filter increases from 1510 nm to 1514 nm, the transmissivity corresponding to the central wavelength increases sharply from 37% to 90%; when the central wavelength of the flat top filter continuously increases to 1562 nm, the transmittance corresponding to the central wavelength increasing gently from 90% to 97% in the case of different amplitudes. Considering the transmissivity required to exceed 90% in the passband of flat top filter and the cost of ultrasonic generator, the ultrasonic wave with an amplitude of 0.4 nm is selected as the research object. The flat top filter with 5–6 nm central wavelength and 1514–1562 nm tunable flat top filter can be realized by applying ultrasonic wave with the frequency in a range of 6–11 MHz. In the tunable range, the highest insertion loss is only 2.23 dB, the lowest is only 0.78 dB, and the lowest rectangularity is 1.4. In a practical flat top filter with machining error within 5 cm, the deviation of center wavelength, rectangularity, insertion loss and passband bandwidth of flat top filter are all very small. The flat top filter has the characteristics of easy design and integration, flat passband, wide tunable range, stable passband bandwidth, low insertion loss and high quality factor. It has important applications in optical communication fields such as optical switch, tunable fiber laser and fiber sensing.