We report a novel scheme to optimize the focusing condition for real-time, swept-source optical coherence microscopy. The axial and lateral behaviors of four-zone binary-phase spatial filters are presented numerically. A nearly constant axial intensity distribution along an extended depth of focus of 1.5 mm and a lateral resolution of 5 microm are experimentally verified. The A-line scan rate is up to 16 kHz, yielding a frame rate of 25 Hz and 640 lines per image.