Both specialized in renewable energy, a focus of Khosla Ventures, but one that has been slow to reap big returns.
Kinnier will start his own company, a move founding partner Vinod Khosla called "standard". It was unclear what Kim intends to do upon leaving the venture capital house, which has backed Jawbone-headset makers Aliph and biofuels company Kior.
"Junior folks join for three years typically and then start companies," he wrote to Reuters in an email. "We have our core set of five partners and though we don't preclude junior partners becoming senior partners, we expect the majority of them to leave to start companies."
Kinnier declined to comment, referring Reuters instead to Khosla, who said the former Google executive always intended to leave the venture capital outfit after a few years to start his company.
Kim did not respond to requests for a comment.
The departures leave the firm with seven partners, including Khosla, a co-founder of Oracle's Sun Microsystems. In May, Khosla Ventures filed to raise a $1.05 billion fund.
Khosla Ventures lost partner Gideon Yu earlier this year when he joined the San Francisco 49ers pro football team as chief strategy officer. His high-profile investments included Square, Twitter co-founder Jack Dorsey's payments company.
After that, the firm hired partner Ryan Kottenstette, who has a background in lithium-ion batteries.
"Hiring is always a continual process for us at the junior level," Khosla said.
Kinnier joined in 2008 from Google and Kim joined in 2009 from venture firm CMEA.