To investigate changes of the macular and peripapillary choroidal areas after trabeculectomy. This prospective and interventional study examined 74 eyes of 74 patients with glaucoma uncontrolled by medical therapy. Enhanced depth imaging optical coherence tomography (EDI-OCT) recorded macular and peripapillary choroidal images at 1 day before trabeculectomy and at 2 weeks after surgery. The Niblack method was used to covert luminal and interstitial areas to binary images. At baseline, the mean intraocular pressure (IOP) was 17.6±6.3 mmHg, while it was 6.5±2.9 mmHg after trabeculectomy (P < 0.001). Increases were observed for the macular choroidal area after the surgery, with the total area increasing from 317,853±95,728 μm2 to 368,597±104,393 μm2, while the luminal area increased from 210,355±73,650 μm2 to 249,464±77,195 μm2, and the interstitial area increased from 107,498±27,613 μm2 to 119,133±31,811 μm2 (all P < 0.001). Increases were also observed after the surgery for the peripapillary choroidal area, with the total area increasing from 1,629,440±460,429 μm2 to 1,974,289±500,496 μm2, while the luminal area increased from 920,141±328,690 μm2 to 1,179,843±357,601 μm2, and the interstitial area increased from 709,299±153,179 μm2 to 794,446±169,029 μm2 (all P < 0.001). There was a significant increase in the ratio of the luminal to choroidal area in the macular area (67.2%) and in the peripapillary area (59.1%). Factors associated with the changes in the peripapillary choroidal area included decreases in the diastolic blood pressure and IOP. A reduction in the IOP after trabeculectomy led to increases in the macular and peripapillary choroidal areas. Observed changes in the choroidal area after trabeculectomy are primarily due to increases in the luminal areas.