Syria's 1-0 victory on Thursday shocked fans in the Chinese city of Xi'an who took to the streets.
China has said it wants to become a "world football superpower".
But the loss means the team could now miss out on a place in the 2018 World Cup in Russia.
China is ranked 78th in the world whereas Syria is 114th, just ahead of North Korea. The Chinese team faces Uzbekistan on 11 October which will decide if they qualify.
Tencent's sports website said large group of fans gathered on the streets outside the Zhuque stadium, demanding the resignation of Cai Zhenhua, president of the Chinese Football Association after the game.
"Resign, resign, resign!", they are heard shouting in a video posted to Twitter.
Online, fans were equally critical of the Chinese team's performance.
"The Syrian football team has proved that we aren't strong and victorious," said one user on micro-blogging site Weibo.
"I'm going to hide my face now," said another.
"My blood pressure literally rose when I was watching the game," a user said.
"Syria, a war-torn country who can't even afford to buy their own shoes or shirts, whose manager earns a monthly salary of 2000 yuan, defeated China whose players earn millions," one person said.
Syria, who play their home matches in Oman due to the war, has seen almost five years of armed conflict.
Earlier this year, China laid out an ambitious plan to become a "world football superpower" by 2050.
The country's President Xi Jinping, a football enthusiast, previously said he wanted China to win the World Cup in 15 years.
The country also wants 50 million children and adults playing the game by 2020.
"The president of the country is pushing for football," Sven-Goran Eriksson, who coaches the Chinese Super League, told the BBC earlier this year.
"He wants China as a national team to be big, to be better in football."
Angry Chinese fans have called for the resignation of the president of China's football association, after the country lost to Syria in a World Cup qualifier.