Blast Works comes with a powerful editing tool that allows extensive customization to the game. Players can construct their own ships, enemies and bosses with the editor, as well create their own backgrounds.

When designing enemies, the player can manipulate projectile patterns, sound effects, movement patterns, hit boxes, and more in the Ship Editor portion of the Blast Works Editor. The player also has the option of fully customizing the ship that they play as. For example, the ship builder lets the player view their ship from many different angles, allowing them to add new pieces, such as wings or weapons, simply by adding shapes to their ship. The basic shapes can be combined to create even more complex constructs, and there are a few moving shapes the player can add to give their ship a bit more life. The player is also given full control over the size, shape, and color of any object they create. This ranges from their main ship to buildings created for custom levels and even enemy craft.

The level designer (the same tool the game's developers used to create the built-in levels that come with the game) also features powerful capabilities. The player can set the basics, such as color scheme or background, then drag and drop enemies into their custom level from either a list of pre-built enemies or custom ships previously created. The player can also set trigger events that can change the orientation of your ship, the behavior of enemy ships, or the movement of the game camera. The player can also add a number of different special effects to their level such as a Virtual Boy-like effect, which turns everything in the level to red and black, or a water effect, to make background oceans or the level itself appear underwater. After constructing a level, the player can preview it before importing it into the game