Superior Court Judge Michael Pastor said the photos, one of which shows Jackson clothed and another one with him nude, are not graphic or gruesome.
Prosecutors said the pictures illustrate the coroner's description that Jackson was thin, but in excellent health.
Defense attorneys objected to the photos, arguing they were gory and unnecessary.
Murray has pleaded not guilty to involuntary manslaughter in Jackson's death. He's accused of giving the pop star a lethal dose of the anesthetic propofol at his rented mansion in June 2009.
Murray's attorneys have suggested in recent months that the singer may have given himself the fatal dose.
The judge also ruled that prosecutors can show limited clips of Jackson's final rehearsals for a planned series comeback concerts in London.
Prosecutors said two clips from the movie "This Is It" will show the pop star was active and energetic, even in the last song he would sing, "The Way You Make Me Feel."
Defense attorneys objected to showing the film footage, claiming it was edited to present the singer in the best light. They noted that Jackson wears different outfits in the video, which shows that not all of the footage was shot in the two days before Jackson's death on June 25, 2009.
A key issue for the defense is Jackson's finances. Murray's attorney, Ed Chernoff, told the court that there were 38 lawsuits against Jackson when he died.
Chernoff said the singer owed $40 million to AEG and hadn't filed with the IRS in three years. Chernoff said the comeback tour Jackson was rehearsing for made the singer take desperate measures to sleep, which motivated him to take the propofol on his own.
Pastor also ruled that prosecutors can have some of Murray's mistresses testify during the trial, but that they should omit some salacious details. For instance, Pastor said he didn't want to hear any references to the strip clubs or gentlemen's clubs where Murray met some of them.
Opening statements were scheduled for May 9.
The Associated Press contributed to this story.