Reinforcing composite materials with carbon nanotubes (CNTs) has the potential to improve mechanical and/or multifunctional properties due to their nano-size. Research has been done on using CNTs to reinforce the interlaminar strength of carbon fiber reinforced composites (CFRPs), but most of the previous work is about randomly oriented carbon nanotubes. Currently, one of the main challenges regarding CNT integration into polymers is mitigating their agglomeration and controlling their dispersion in the polymer matrix. By aligning CNTs with an external field, more tailored structure control can be achieved, and a better understanding of how CNT agglomeration and dispersion relate to external field application and CNT concentration is needed. In this work, we studied the effects of magnetic field magnitude, CNT concentration, and matrix viscosity on CNT agglomeration and morphology. We measured the fracture toughness reinforcement of epoxy-CNT nanocomposites at various CNT concentrations (0.1 vol.% and 0.5 vol.%), magnetic field magnitudes (no field, 180 G, and 300 G), and matrix viscosities (older epoxy-hardener system with higher viscosity and newer epoxy-hardener system with lower viscosity). Our results demonstrated that aligning CNTs with a magnetic field can lead to extra reinforcement when compared to using randomly oriented CNTs if the field magnitude, CNT concentration, and matrix viscosity are selected accordingly. The maximum fracture toughness reinforcement achieved with the higher viscosity epoxy-hardener system (~72%) was with 0.5 vol.% of CNTs with a 180 G field, whereas the maximum reinforcement with the lower viscosity epoxy-hardener system (~62%) was observed for the samples fabricated with 0.1 vol.% of randomly oriented CNTs. COMSOL simulations were also conducted to understand the behavior of CNT agglomeration and alignment at different field magnitudes and CNT concentrations, and were compared with the experimental results. To maximize CNT reinforcement, more work needs to be conducted to address the challenge of CNT agglomeration and dispersion control in a polymer matrix, such as a more in-depth study of how different field magnitudes affect fracture toughness improvement and new methods to improve CNT dispersion.