Micro aerial vehicles (MAVs) usually suffer from several challenges, not least of which are unsatisfactory hover efficiency and limited fly time. This paper discusses the aerodynamic characteristics of a novel Hex-rotor MAV with a coaxial rotor capable of providing higher thrust in a compact structure. To extend the endurance during hover, flow field analysis and aerodynamic performance optimization are conducted by both experiments and numerical simulations with different rotor spacing ratios (i = 0.56, 0.59, 0.63, 0.67, 0.71, 0.77, 0.83, 0.91). The measured parameters are thrust, power, and hover efficiency during the experiments. Retip ranged from 0.7 × 105 to 1.3 × 105 is also studied by Spalart–Allmaras simulations. The test results show that the MAV has the optimum aerodynamic performance at i = 0.56 with Retip = 0.85 × 105. Compared to the MAV with i = 0.98 for Retip = 0.85 × 105, thrust is increased by 5.18% with a reduced power of 3.8%, and hover efficiency is also improved by 12.14%. The simulated results indicate a weakness in inter-rotor interference with the increased rotor spacing. Additionally, the enlarged pressure difference, reduced turbulence, and weakened vortices are responsible for the aerodynamic improvement. This provides an alternative method for increasing the MAV fly time and offers inspiration for future structural design.