requests is third-party, so (per the style guide) there should be a blank line in the imports:
import os
import requests
api_repo is constant, so should be API_REPO. There should also be spaces around the = in assignments:
API_REPO = 'https://api.github.com/user/repos'
Explicit line continuation isn't very Pythonic, especially when the line is short enough anyway:
url = '%s?access_token=%s' % \
(api_repo,API_TOKEN,)
Also, there should be spaces after commas (and I wouldn't bother with the trailing one). This would be better written as:
url = '%s?access_token=%s' % (API_REPO, API_TOKEN)
r and i aren't very good variable names. I would use req_json and git_url.
You are mixing % string formatting with + concatenation. You should at least be consistent, and I would use the more modern str.format:
os.system("git clone {}".format(git_url))
You should also be consistent with string literal quotes. Per the style guide:
In Python, single-quoted strings and double-quoted strings are the same. This PEP do [sic] not make a recommendation for this. Pick a rule and stick to it. When a string contains single or double quote characters, however, use the other one to avoid backslashes in the string. It improves readability.
In all, I would probably have written it as:
import os
import requests
API_TOKEN = "..."
API_URL = "https://api.github.com/user/repos"
url = "{}?access_token={}".format(API_URL, API_TOKEN)
req_json = requests.get(url).json()
for repo in req_json:
os.system("git clone {}".format(repo["git_url"]))
