Here are some recommendations for science fiction Christian books. Also, check out my lists for Christian fantasy, superhero/zombie, historical, and general fiction.
Out of the Silent Planet, Perelandra, and That Hideous Strength, a great trilogy about the space travel and sin and innocence and such. The second one is probably my favorite. Only barely sci fi, closer to a kind of fantasy.
The Search for Fierra and Siege of the Dome are a pair of books about investigating a lost planetary colony that has split into extreme factions. The Christianity is very subtle.
A realistic use of a NASA moon landing reveals a sci fi/biblical fantasy mystery. Can't say anything else without spoiling it.
There's treachery on the first expedition to Mars, and a Christian must wrestle with the question of life on the planet. This and the sequel, The Fifth Man, are survival thrillers.
The first in the Lamb Among the Stars trilogy. It's a futuristic intergalactic society that exists after an eschatological event where sin is almost non-existent. But then a darkness appears. This isn't bad, but sinless characters do feel a little two-dimensional.
The first of the Dark Trench Saga. In a future-Islamic world, a worker with a wifi-connected brain finds evidence of a greater truth while debugging a robot that just came back from an experimental deep space voyage. A second trilogy in this world has begun with this book. But my favorite from this author would be Mask.
Vampires are loose on an Amish space colonization ship! In spite of the awesome title and cover, this is played totally straight. It's good, but I actually might have preferred it to be more like a terrible B movie.
Futuristic war action trumps characters in this really fun speculative world where a small Calvinist country is overrun by an Islam-ish power.
Kind of like Star Wars with a class of people with special powers, but from a woman's point of view and more politics than action.
An odd but interesting story of an alien finding Christ that's left pretty open-ended. It was coauthored by a Mormon, but there's no Mormonism in it. It does wax a little mystical about a crucifix.
YA dystopian.
Dystopian.
Two sets of characters see change happen in a post-Christian space opera world. There's a bit of weakness in the first set, but the political/sci fi military stuff comes in to elevate it and make it much more epic.
This light series uses some old sci fi tropes but turns them into a comedy. The main character is like Han Solo/Kirk/Star Lord mashed up and goofier. Fun.
This is a really interesting collection of short stories of the history of robots programmed to love God. It does a good job of exploring the questions a universe like this would have in a short space, and even gets a little crazy. Super fun read.
Supraphysica by Drew Boudreaux
A pretty bizarre premise of people supernaturally creating a new planet on behalf of God. There's not really a traditional antagonist or plot, but the character arcs make it work somehow. Enjoyable.