From the perspectives of nature, human, and carrying capacity and applying the entropy and linear weighted comprehensive methods, this paper constructed an evaluation system to assess the vulnerability of agricultural water resource in Henan Province from 2001 to 2016. In addition, this paper also examined the main obstacles affecting the vulnerability. Results show that the vulnerability of agricultural water resource in 9 cities in Henan Province decreased from 2001 to 2016, while it increased in the other 9 cities; and the vulnerability growth rate varied significantly. The evolution trend of vulnerability could be divided into four types: increasing first and then decreasing, decreasing first and then increasing, increasing with some fluctuations, and decreasing with some fluctuations. The vulnerability of agricultural water resource in Henan Province illustrated a concentrating characteristic in its spatial distribution with the decreasing order as follows: Northern Henan, Eastern Henan, Southern Henan, Central Henan, and Western Henan. The vulnerability of agricultural water resource in municipalities was mainly affected by human and carrying capacity, and the main obstacle factors were different. In order to achieve the coordinated development of agricultural production and water resource utilization in Henan Province, this paper suggests that human intervention in water resource system should be positively strengthened by increasing investment in agricultural funds, improving the level of farmland water conservancy construction, and promoting agricultural water use efficiency.