Shelton, 33, of Brodhead received the maximum prison sentence plus 10 years probation from Green County Circuit Court Judge James Beer.
"He won't hurt anyone again, but it doesn't bring my son back," said Christopher's mother, Amy Uptegraw, after the sentencing.
Shelton was convicted Jan. 17 for the death of his son at their Decatur Township residence.
Shelton has been in the Green County Jail since May 2007. The jail time will be applied toward Shelton's prison term.
He was sent Monday to Dodge Correctional Institution in Waupun.
"The citizens of the state are entitled to expect you to obey the law," Beer said before sentencing Shelton. "They have a right to know criminal behavior will be punished."
Shelton, who didn't testify at his trial, addressed the court through a statement read by his attorney, Katherine Findley. Shelton said he wished he had taken Christopher to the doctor in the days before he died.
"It was obvious he wasn't feeling well," Shelton said in the statement.
Shelton maintains Christopher could have died from a vaccination he received two weeks before his death, or from choking on his own vomit.
But evidence presented during Shelton's trial showed Christopher died from traumatic brain injuries caused by being violently shaken. Shelton was at home alone with his twin sons, Christopher and Charles, in the hours before calling 911 to report Christopher wasn't breathing.
Shelton said Monday the impression he showed no feelings about his son's death was because he was too busy defending himself. He said his actions didn't show how he felt about Christopher.
"Christopher was my little buddy. He's with me now as he always will be. Christopher and God know how much I love them."
Monday, Shelton was dressed in an orange Green County Jail jumpsuit, his hands and feet shackled.
He showed little emotion throughout the hearing, but wiped tears away from his eyes when his mother spoke on his behalf.
Two different images of Shelton were given Monday.
To the family of Shelton's live-in girlfriend, he was someone who needed to be sent to prison for a long time.
"He's a monster who entered our lives and left us with a nightmare that will never end," said Keri Rajiroski, Uptegraw's aunt. "My sister lives with the guilt of not being there when her son needed her the most."
Uptegraw told the court Shelton was to blame for what happened to Christopher, and said he deprived her and her family the right to see Christopher grow up.
During the trial, Uptegraw testified that Shelton was abusive to her and the children.
Shelton's family said he was a good person whose life has changed since he's been in jail.
"He's a loving, caring father, brother, nephew and son," his sister, Barb Vittetoe, said. "None of us can understand what he's gone through."
Findley asked the court to impose a 10-year prison sentence with 20 years probation. She said Shelton would face the consequence of prison if he violated his probation.
Green County Assistant District Attorney Jeff Kohl asked the court to sentence Shelton to the maximum term.
"Doing anything less would weaken the seriousness of the crime," Kohl said.
In three months, Shelton is scheduled to stand trial for abusing Christopher's twin brother, Charles.
Shelton is charged with two counts of child abuse in relation to injuries Charles sustained.
Shelton faces up to 16 more years in prison and up to $25,000 if convicted of those charges.