Objectives The development of organic farming offered the possibility of coordinating ecological conservation and economic development in nature reserves, and this study sought to scientifically assess the ecological effects of organic farming in the crested ibis habitat from a regional perspective.

Methods This study used GIS spatial analysis as a base tool, combined three methods of land use change analysis, habitat quality analysis, and ecological sensitivity analysis with the means of spatial visualization analysis, to investigate holistically whether the development strategy of organic agriculture as the leading industry in the ibis habitat was beneficial to the local ecological environment.

Result The results showed that after years of ecological protection and sustainable development of organic agriculture, the area of forest, paddy field, and the water area of the local land-use types suitable for breeding and foraging of the crested ibis have been expanded, with a total expansion of 21.56 km² in the twenty years from 2000 to 2020. In 2020, the area has occupied a total of 79.71% of the county’s land area, which could be the evidence of the effectiveness of local biodiversity conservation and has laid the foundation for the development of organic agriculture. After more than ten years of organic farming development, the regional habitat quality was still at high level, the overall habitat quality index amounted to 0.768 and can provide enough resources and space for the breeding of the crested ibis and biodiversity conservation. And in the face of possible future ecological and environmental problems, the ibis habitat showed some resilience, overall ecological sensitivity was moderately low, with the largest area of moderate sensitivity, especially in the main production areas of organic agriculture, which showed a promising performance of high habitat quality and low ecological sensitivity.

Conclusions The study confirmed that organic agriculture produced a positive effect on the ecological environment, ensured the sustainability of land use, safeguarded the quality of habitats, and guaranteed the healthy development of ecosystems, making it possible to harmonize ecological protection and economic development and to open up the cyclic paths between the green hills and the silver mountains.