Plateau wetlands play an important role in social and economic development and ecological security. The ecological environment of a plateau wetland is fragile and vulnerable to external interference, resulting in changes in the wetland structure and ecological functions. Ecological security assessment of plateau wetlands is the key to fully understanding their ecological security situation. Yunnan Province, which is located in the Qinghai-Tibet Plateau, has a significant stereoscopic climate, which is characterized by distinct features of diverse and complex wetlands. Thus, studying the wetland ecological security of Yunnan Province spanning various climatic zones is of great significance. In this study, an improved pressure-state-response model was constructed, and an index system containing state and social pressure was established using remote sensing data, Yunnan Province Yearbook data, and socioeconomic statistical data. Taking 16 prefectures in Yunnan Province as samples, this study weighted the evaluation indices via the combination of entropy weighting and expert weighting. In addition, the wetland ecological security state in Yunnan Province in 2017 was evaluated using the fuzzy matter-element method, and the influencing factors were analyzed. Results showed that the highest ecological security index of wetland was distributed in Nujiang, Diqing in the northwest of Yunnan Province and Xishuangbanna in the south, whereas the lowest area was in Qujing, Zhaotong in the northeast of Yunnan Province and Baoshan in the west. Differences were observed in the influencing factors of wetland ecological security in different prefectures. In general, the influencing factors in Yunnan Province were the annual average temperature, proportion of natural wetland, percentage of secondary industry, annual precipitation, wetland ecological service function per unit acreage, fertilization intensity, and industrial water recycling rate. The results of grey correlation analysis showed that climatic factors and human disturbance activities were the main influencing factors of wetland ecological security in Yunnan Province, and the influence rate of the two was close to each other. The findings of this work could provide suggestions for the decision making on ecological security development in plateau wetlands across multi-climate zones, as well as data support for the ecological protection of plateau wetlands.