You don't shut down lee sin, he is just too damned powerful, you ENDURE Lee sin. Try not to feed him, wait for 'Lee Syndrome' to kick in. THen he lands a q on your annie mid under tower, and goes in for the insec, only to get Tibberised and shut down.
Late game you have a fighting chance against him. He does fade late game, meaning he gets down to the same power level of everyone else. (He was balanced a year ago, but received a gentle series of buffs, and the new jungle suits him so well). Late game, either he builds pure damage, in which case, you pray you have reliable, preferably non skillshot, hard CC on your team, and explode him before he takes all all of your carries single handed, which he will do, if you lack CC OR, more dangerously, he builds bruiser, dives your team, kicks out a carry to his team, and wins the teamfight. This is more scary, and require more hard CC to prevent.
A juggernaught top or jungle can stop him split pushing past midgame if he builds thornmail. If you have delicate fighters or assassins top and jungle, you're in deep trouble.
Oh yes, he also has a real vulnerability to exploit. His soaring winrate makes him very vulnerable during the ban phase, hit him then....