We study two aspects of 3D QCD with massless fermions in a holographic set-up from string theory, based on D3/D7 branes; parity anomaly and baryons as baby Skyrmions. We first give a novel account of parity anomaly of 3D QCD with odd number of flavors from the IR holographic viewpoint by observing a subtle point in D7 brane embeddings with a given fixed UV theory. We also discuss its UV origin in terms of weakly coupled D-brane pictures. We then focus on the parity-symmetric case of even number of N_F flavors, and study baryons in the holographic model. We identify the monopoles of U(N_F) gauge theory dynamically broken down to U(N_F/2)x U(N_F/2) in the holographic 4 dimensional bulk as a holographic counter-part of 3D baby-Skyrmions for baryons in large N limit, and work out some details how the mapping goes. In particular, we show that the correct baryon charges emerge from the Witten effect with a space-varying theta angle.