Shami, who is expected to lead India's pace attack in the upcoming cricket World Cup in England and Wales, has been locked in a protracted legal battle with Hasin Jahan since March 2018.
Jahan, a former model, publicly accused Shami of having numerous affairs and harassment.
"The chargesheet has been filed against Shami under IPC 498A (for mental and physical torture, and dowry harassment) and 354A (for sexual harassment and assault," Dip Narayan Pakrashi, public prosecutor in the eastern city of Kolkata, told AFP.
"If charges are proved (in court), the punishment may amount to five years imprisonment and fine," Pakrashi added.
Shami has dismissed all the accusations as a campaign to defame him.
Jahan has also accused Shami of corruption.
The Board of Control for Cricket in India (BCCI) had withheld Shami's contract pending a review into a series of allegations made by his wife, including corruption and even attempted murder.
Shami was soon cleared of corruption charges by the BCCI and offered an annual retainership contract by the world's richest cricket board.