In order to improve the control performance of the nanopositioning and nanomeasuring machine (NPM) system, the microtribological behavior of thin fluorocarbon (FC) film under water lubrication was investigated by a microtribometer based on laser interferometers. Experimental results indicate that, on the transition from rigid to soft contact, the friction force under water lubrication firstly decreases and then increases. It is thought that the contact property plays a role in determining the microtribological properties. A simple physical explanation is provided based on the lubrication and mechanics theory. A systematic characterization of the frictional properties of the FC film is crucial for the further development of the NPM system.