Molecular electronics aims at integrating controllable molecular devices into circuits or machines to realize certain functions. According to device configuration, molecular field-effect transistors with top-gate electrodes have great advantages for integration. Nevertheless, from technical aspects, it is difficult to control lateral scale and position of a top-gate electrode precisely. Therefore, one problem arises in how lateral scaling and positioning effects of a top-gate electrode affect device performance. To solve this problem, the electronic transport properties of single-molecule field-effect transistor configurations modulated by a series of partial-scale top-gate electrodes with different lateral scales and positions are studied by using non-equilibrium Green’s function in combination with density functional theory, and compared with those of the full gate electrode (can be considered as a bottom gate electrode). The results show that lateral scaling and positioning effects indeed have a great impact on electronic transport properties of single-molecule field-effect transistor configurations. For -saturated 1,12-dodecanedithiol devices, larger lateral scale of a partial-scale top-gate electrode obtains larger amplification coefficient (ratio of device conductances with/without a gate electrode), and even larger than that of the full gate electrode. While lateral positioning effect has little influence on this device. For -conjugated 1,3,5,7,9,11-dodehexaene-1,12-dithiol devices, performance of a partial-scale top-gate electrode mainly depends on locations of its two edges, i.e. the number of bonds that it breaks. These results will provide theoretical directions in device designing and manufacturing in the future.