The basketball association writes on its website that he is leaving for personal reasons.
Hugo Lopez is replaced by assistant coach Kenny Grant Jr.
"We respect that Hugo must leave at this time and do not want to comment on this more than that there are personal reasons behind it," said Secretary General Fredrik Joulamo in a statement and continues:
"We have full confidence in Kenny who has been with Hugo from the start during the previous European Championship qualifiers and he will, together with the rest of the staff and the players, lead this in goal in a good way."
Sweden has played two of four matches in the pre-qualifiers which will decide whether the national team advances to the regular World Cup qualifiers.
In the first match, there was a loss against Portugal by just under 77-79, then Sweden bounced back and took a comfortable victory against Luxembourg (129-76).
The two best teams in the group advance to the World Cup qualifiers.
The next match is played against Portugal on Monday.