As with much in science, it is best to talk in terms of "models" rather than what something is. We can model a photon, for example, as a quantum excitation of the electromagnetic field.
Space is part of the model for doing physics. Together with time it is a coordinate system to describe locations, and the distances between locations.
The simplest model is "Euclidian" in which the positions are described by triplets of numbers $(x, y, z)$ and distance is $\sqrt{x^2+y^2+z^2}$.
This is especially important in General Relativity as the "curvature of spacetime" is defined in terms of formulae for describing the distance between points (a "metric"). In relativity spacetime is $(x,y,z,t)$, and the distance has a more complex defintion.
You can conceive of empty space, and it is useful in some situations. In particular there are important metrics that apply to empty space: The Minkowski metric of flat space, and the Schwatzchild metric of empty space around a point mass.
So what is space(time), is a question for philosophers. How do we describe, use and model spacetime is a practical question with a specific answer. We can describe and model space using a coordinate system.