A protective carbon film, prepared by electron-cyclotron-resonance (ECR) plasma sputtering, has attracted considerable interest because the film can possess both the high wear durability and the high conductivity without doping. Such properties can be obtained, for example, when a negative bias voltage V_B (−40≤V_B≤−140 V) is applied to a substrate made of silicon. Little is known, however, about the atomic structure and bonding state of the ECR films for such a bias region, so that the physical origins of the macroscopic properties are not fully understood. In the present study, electron energy-loss spectroscopy (EELS) in a transmission electron microscope has been applied to investigate such ECR films that were deposited on a sodium chloride substrate for three different bias voltages: 0 V, −75 V and −120 V . The physical density of each ECR film was found to be lower than that of graphitized carbon and that of amorphous carbon. For each of the ECR films, the fraction of sp² bonding was estimated to be more than 90%. The carbon clusters with sp² bonding were considered to be more ordered for V_B=−75 V and −120 V than for V_B=0 V . The averaged density of valence electrons did not change much for each film, but the band structure is considered to vary depending on a local area. For the film prepared by the ECR technique, the macroscopic properties of the film such as electronic and mechanical ones may be controlled by controlling the ordering of sp² clusters.