The phrase suggests the person has many good qualities, by emphasizing what they lack. Despite the rumors, I knew she didn't have a mean bone in her body.
Pro Tip 2/3
Metaphorical
The phrase is not literal; bones represent innermost qualities, not physical bones. Even when provoked, he shows patience and doesn't have an angry bone in his body.
Pro Tip 3/3
Strong Emphasis
Use the phrase to strongly emphasize the absence of a negative trait. You can trust her with anything, she doesn't have a deceitful bone in her body.