Direct numerical simulations are performed to investigate turbulent flows in a rectangular duct of aspect ratio varying from 1.0 to 3.0 at a fixed low Reynolds number 150. Persistent secondary flows of Prandtl’s second kind are observed in the corners of the ducts. As the aspect ratio increases, streamwise vortices near the top and bottom walls extend towards to the central vertical plane of ducts. Particularly, the displacement of vortex cores near the top/bottom wall can be described as a function of the distance to the sidewall. Detailed analyses of turbulence statistics including the mean flow, turbulent kinetic energy, turbulent intensities, Reynolds stress budgets, and pre-multiplied one-dimensional energy spectrum are conducted to understand the aspect ratio effects on the flow physics. In the duct of aspect ratio 3.0, hairpin flow structures are present in the central regions of the duct, and their characteristics are similar to those exhibited in the plane channel flows. Furthermore, as indicated by the energy spectra, a spanwise quasi-homogeneous region spans over approximately 270 wall units in the central region of the rectangular duct.