In The Golden Compass, the conflict of the story plays out through a struggle against a powerful and evil group, the Oblation Board (controlled by an even larger evil organization), which seeks to enact mass control over people by severing spirits from bodies. In The Golden Compass, animal familiars accompany people throughout the entirety of their lives. While there is no direct explanation of what these animals represent (though they are called daemons), many readers believe these animals are the physical manifestation of one's soul. In the story, the Oblation Board steals children and their daemons away and tortures the children by severing the bond between child and demon. Once separated, the demon dies and the child is left in a zombie-like state. Lyra Belacqua, a child whose dear friend is stolen by the evil group, leads a rebellion against the Oblation Board. Some have found Christian meanings in the Golden Compass.

There are several important conflicts in "The Golden Compass." What makes this book so great and interesting is the way they interweave—and the way they shift around. There's a conflict between generations (Lyra and the kids/the adults). There's a conflict between self-determination and authority, as happens when the children's daemons are severed from them. There's a conflict between the existing order and change, though that emerges more in the later books. Finally, there's a conflict between heart and head; this happens in several characters. All of these happen amidst an emerging conflict between good and evil.

The conflict in The Golden Compass is simple,  it is a battle between good and evil, with the fate of the universe at stake.

"This type of conflict between free-thinking freedom fighters and authoritarian control is common in fantasy and science fantasy stories."

Lyra Belacqua, the young hero, unexpectedly finds herself in a quest for the truth, on the side of good,  about a mysterious "dust" that connects all people and parallel universes.

"Lyra sees the Master trying to poison Lord Asriel, warns him, and is then taken into his confidence. However, his comments pique her curiosity about many things such as the church and her own history, which she has heretofore taken for granted. When other children start to disappear into the clutches of the mysterious Oblation Board, she becomes even more curious." 

On the side of evil, is the Magisterium, which opposes the mentioning of the dust, they will do anything to keep it from even being mentioned.