In confocal microscopy, the effective optical transfer function (OTFeff) with Gaussian plane wave illumination covers very few high-frequency components, which prohibits further improvement of the resolution. We propose modulated pattern scanning microscopy (MPSM) to achieve super-resolution imaging. In MPSM, the phase of the illumination beam is modulated to reassign the OTFeff in the Fourier domain. The phase mask is designed using an optimization algorithm to obtain the fluorescence emission pattern with rich high-frequency components. Then, the postprocessing algorithms are adapted to retrieve the super-resolved images from the modulated recordings. Simulation and experiment demonstrate that MPSM increases the resolution approximately 1.3 times better than confocal microscopy. Compared with conventional deconvolution, MPSM exhibits a higher signal-to-noise ratio.