This paper takes the limited development ecological zone of Jilin Province as the empirical research area. Based on cross-sectional data of the counties in 2005, 2010, and 2015, we used entropy weight-TOPSIS evaluation method, Markov chain, and obstacle degree model to measure the green development level and its obstacle factors using the indicator system constructed from five dimensions of land space optimization, natural capital utilization, economic development quality, social welfare progress, and environmental pollution control. The results showed that the integrated level of green development in the limited development ecological zone of Jilin Province was at a low level as a whole and with a declined trend. The spatial distribution pattern of the green development level was higher in the northwest and lower in the southeast. The state of green development level transfer in 2005-2010 and 2010-2015 was relatively unstable, and the type of green development level was more obvious. The proportion of science and technology expenditure, the investment in fixed assets, the proportion of construction land, the output rate of construction land, the number of middle school students, the output rate of cultivated land, the output rate of forest land, and the removal rate of chemical oxygen demand were the main obstacle factors restricting the level of green development. Finally, the paper put forward some countermeasures and suggestions such as constructing ecological industrial system, increasing investment in green science and technology, improving the efficiency of land intensive use, and improving the ecological compensation mechanism.