Black, who made his international debut last year while playing with Rangers in the Third Division, is alleged to have bet on 160 Scottish matches over seven years, including three where he bet against his own club winning.
The 28-year-old Rangers midfielder is accused of betting on matches between March 4, 2006, and July 28, 2013, when he was also playing for Hearts and Inverness Caledonian Thistle.
On top of the three against his own club, Black is accused of betting on 10 games that involved the club he was with which did not affect the end result and 147 Scottish matches he did not play in.
It comes as Laxey Partners Limited, which is now one of the main shareholders of Rangers after buying one million shares, is to vote in favour of removing directors from the club.
But the firm is not going as far as backing the three supporters groups who have challenged the board to remove former chief executive Charles Green from his role as a consultant at a board meeting tomorrow.
The SFA, which stressed there is no evidence of match-fixing by Black, would not divulge which of the three clubs Black is accused of betting against.
On the first date mentioned in the notice of complaint, Black played 90 minutes for Inverness in a 1-0 home defeat by Motherwell, which cut Caley Thistle's lead over the Lanarkshire side to three points in the race for a top-six place in the Scottish Premier League.
The final date in question saw the 28-year-old score in a 4-0 Ramsdens Cup victory for Rangers against Albion Rovers.
The SFA took action after major players in the betting industry raised suspicions with Scottish football's governing body in the past couple of weeks. Betting on other matches was discovered following further investigations.
Black, who can carry on playing for Rangers, has until August 26 to respond to the complaint. A hearing has been set for September 12.
An SFA spokesman said: "It is the first time in Scotland there has been a case like this that there has been evidence to allow it to go to a panel.
"There is sliding scale of sanctions and at the top end is a £5,000 fine and/or a suspension. It talks of suspension or expulsion from participation in the game but that is an absolute maximum. The panel will look at every case and take into account mitigating or aggravating circumstances."
Mr Black is accused of breaking SFA Rule 33 which states that no player shall bet "in any way" on a football match except authorised and registered football pools.
A Rangers spokesman said: "The club is aware of the SFA's Notice of Complaint and is currently investigating the matter."
The governing body also stated there was no evidence to suggest any breach of Rule 23, which prohibits players and officials knowingly behaving in a "manner, during or in connection with a match in which the party has participated or has any influence, either direct or indirect, which could give rise to an event in which they or any third party benefits financially through betting".
The former Blackburn trainee signed for boyhood heroes Hearts in July 2009 and left for Rangers last summer as a free agent after the Tynecastle club slashed their wage bill.
The combative player was Ally McCoist's first signing in the summer of 2012 as Rangers were demoted to Division Three after the 140-year-old club went into administration.
Black made his only Scotland appearance in the dying minutes of their match against Australia in August 2012. He famously worked as a part-time painter and decorator in December 2011 to help pay bills when his Hearts wages were overdue.
Last week Stoke City's Cameron Jerome was fined £50,000 after he admitted breaching betting rules. But the charge did not relate to games he was involved in.
In June, Tottenham midfielder Andros Townsend missed playing for England Under-21s in the European Championship after he was fined £18,000 and banned for four months, three of those months suspended, for a breach of betting regulations.