Highway construction is crucial for regional economic and social progress; yet, it presents considerable ecological challenges, including habitat disruption and exacerbated soil erosion. Conventional linear transportation infrastructure projects focus on evading ecologically sensitive zones, such as nature reserves, scenic areas, and watershed protection regions. Additionally, they enforce erosion control strategies, encompassing protective installations and drainage networks. These efforts are heavily dependent on standard regulations and the expertise of designers. A principal challenge is that prevailing standards tend to be principle-based, concentrating more on post-construction environmental rehabilitation than offering quantitative benchmarks and techniques for preemptive ecological preservation. To address these issues, this study introduces a set of evaluation indicators and a decision-making framework designed to assess the ecological impact of highways. The aim is to integrate proactive ecological conservation measures into the early planning and design stages of highway projects. The evaluation indicator system innovatively accounts for not only the conventional metric of area encroachment in ecologically sensitive areas but also the highways' influence on ecosystem services, including habitat quality, water yield, and soil erosion. With a focus on the Qinghai-Tibet Plateau region, the effects of highways on permafrost are additionally a crucial factor to consider. Consequently, the evaluation system includes indicators like the extent of permafrost and medium-thickness seasonal frozen soil impacted by route choices, the regions of grassland and forestland encroached upon, alterations in habitat quality, water yield, and soil erosion within the zones influenced by roads. To tackle the challenges of integrating qualitative and quantitative attributes, ambiguous attribute grading thresholds, and complexities in decision-making based on analogous reasoning within the multi-attribute decision-making framework, a multi-dimensional and multi-rule cloud model has been developed. This model evaluates and decides on route options from a low ecological impact perspective, based on the established indicator system. It categorizes all evaluation indicators and results into three levels, calculates the corresponding numerical features of the cloud model, determines the membership degree and evaluation indicator score through rule generators, and finally calculates the total score of route options through weighted summation for ranking and decision-making. Subsequently, the evaluation and decision-making method for low ecological impact was applied in the planning of the Jiuma Expressway. The results indicate that the preliminary design phase and the detailed design phase for construction drawings of the Jiuma Expressway achieved scores of 0.489 and 0.483, respectively. It was observed that by optimizing route schemes, utilizing bridges and tunnels instead of embankments, enhancing slope protection, and reclaiming temporary land, the ecological disturbance caused by construction can be significantly reduced. The study proposes a method for evaluating and deciding on low ecological impact in highway construction, facilitating a shift from post-recovery to proactive planning and protection of the ecological environment. This method provides decision support for highway design optimization, ecological risk monitoring and management, and ecological protection policy-making, thereby fostering regional ecological protection and sustainable development.