Habitat change features prominently in maintenance of species population and human security. Understanding the roles of historical habitat change in species protection are crucial for habitat management or restoration and evaluating effectiveness of species conservation. However, due to lack of spatially unbiased species occurrence data, mapping long-term changes of the endangered species' habitats remains unsolved. In this study, taking the range of Menghai-Lancang Asian elephant herd with frequent human-elephant conflicts as an example, a new habitat suitability evaluation method for mapping long-term changes of habitat was proposed. A total of 15 habitat evaluation factors were selected by meta-analysis. Based on the contribution rate of each evaluation factor to habitat quality derived from the MaxEnt model driven by Asian elephant occurrence point, we combined a habitat suitability index (HSI) model and the MaxEnt-derived contribution rates of habitat evaluation factors to evaluate the Asian elephant habitat suitability from 1988 to 2020. Based on the resultant long time-series habitat suitability of Asian elephants, we analyzed spatio-temporal dynamics of Asian elephant habitat and the relations between human-elephant conflicts and habitat landscape changes. Results show that: (1) under the premise of unchanged habitat preferences of species in the study period, the MaxEnt model and the HSI model could be integrated for the long-term habitat evaluation with the inherent relations between the habitat use of species and the environmental factors; (2) The area of existing suitable habitat accounted for one third of the study area (4039.76 km²), which were mainly distributed along the main streams of rivers (such as the Lancang River, Nanlang River and Nanlan River), and the habitat suitability decreased with the distance apart from the river; (3) The highly suitable habitat for Asian elephants decreased by 4.7% (568.48 km²) from 1988 to 2020, in which about 3% (362.89 km²) were lost from 2000 to 2013; the connectivity of habitat patches decreased significantly, especially for the optimum habitat patches; conversely, the number of habitat patches increased by 10.8%, indicating that habitat landscape fragmentation worsened; (4) The area of the degraded habitat accounted for 9.11% (1094.21 km²) in the study area from 1988 to 2020, and human elephant conflicts mainly occurred in the habitat degraded areas; moreover, habitat degradation and habitat fragmentation caused by human activities and modifications of natural environment were the main factors for the occurrences of human-elephant conflict accidents. Therefore, rehabilitating the connectivity of suitable habitat patches are urgently needed for thriving the Asian elephant population, mitigating human-elephant conflicts and boosting ecological civilization construction.