Unverified footage on social media showed a vehicle inside the building with officers pointing their weapons at the driver's door, as people fled down stairs and into the open.
A spokesman for the consulate said the suspect had driven "violently into our consulate's administration hall, posing a serious threat to the lives of staff and people on-site and causing serious damage."
San Francisco Police Department's Sergeant Kathryn Winters said officers responded after being alerted to the vehicle having crashed into the visa office.
"Officers entered, made contact with the suspect and an officer-involved shooting occurred," Winters told reporters.
Officers, paramedics and medics had tried to save the suspect's life, but that the person was pronounced dead at the hospital some time later, Winters said, adding the police could give no details about the suspect's identity.
The local ABC7 News channel said its crews had seen a man covered in blood and apparently unresponsive being taken away from the scene.
"This is an open and active investigation and the San Francisco Police Department is currently working in coordination with investigators from the US State Department," Winters said.
The consulate spokesman said the body "strongly condemns this violent attack and reserves the right to pursue accountability for the incident.
"The Consulate has made solemn representations to the US side, requesting a prompt investigation into the truth and a serious punishment in accordance with the law."
San Francisco is home to a large number of ethnic Chinese residents, including many from Taiwan, a self-ruled island that Beijing considers a renegade province and has vowed to one day control.
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