I found some definition were necessary for me. I tried to remove but I couldn't find the specify command. It's not like npm it has uninstall command can directly uninstall them, so I just remove the ones from tsd.json without typing uninstall command.
Running tsd reinstall --clean will eliminate the definitions not found in tsd.json.
Please note that tsd is deprecated. Consider using typings as your definitions package manager.
Here's how you can uninstall a definition package using typings
typings uninstall <name> [--save|--save-dev|--save-peer] [--ambient]
Options:
  [--save|-S]       Remove from "dependencies"
  [--save-dev|-D]   Remove from "devDependencies"
  [--save-peer|-P]  Remove from "peerDependencies"
  [--ambient|-A]    Remove from the ambient version of dependencies
    [-SA]           Remove from "ambientDependencies"
    [-DA]           Remove from "ambientDevDependencies"
Aliases: r, rm, remove, un
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