Develop your setting, thinking about as many details as you possibly can. According to Writing-World.com, creating a believable, reader-absorbing setting is the most important part of science fiction writing. People choose stories set in space over stories set on Earth because they want to escape into a world completely different from their own. To make your world feel realistic, you'll need to spend time building what other writers can take for granted. Ask yourself what the weather's like and what the cultural, religious and political values of the planet's people are. Remember that you'll need to spend more time developing these details than you would when writing an Earth-bound story.
Ask yourself who your characters are and what they're like. Resources for Science Fiction Writers says that any aliens you create should be aliens. In other words, avoid making "alien" characters who act, look and behave like humans for the exception of pointy ears or squiggles on their cheeks. Aliens might have some human characteristics, but they're probably not exactly like us.
Decide how your characters will interact with each other. If you have humans and aliens making contact, you'll probably need to create different communication systems for both races. Decide if you characters use gestures, language or something entirely different. If you want to avoid the challenge of creating a full, alien language, try setting your story some time after first contact has been made, and aliens have had time to learn human language.
Pencil out the plot for your story, asking yourself why your characters are in space in the first place. Perhaps they're on a mission to colonize space or to mine for new natural resources on foreign planets. Maybe humans have been living on other planets for sometime, and proposed human development is causing unrest among a planet's alien population.
Research plot points that involve science and technology so that you can back your story with real knowledge. Even if your story is futuristic, scientists speculate what might be possible based on existing knowledge, and you can use that information. You don't have to stick rigidly to scientific research, but referencing it in your story can make your tale more plausible.