Short-term instability is one of the key challenges for redox-based resistive random-access memory (ReRAM) reaching practical applications in the field of neuromorphic computing. Developing programming schemes that balance resistance fine-tuning with short-term stability is crucial for improving the reliability of ReRAM devices. In this work, we explore the impact of programming schemes on the short-term variability of valence change mechanism (VCM)-based filamentary ReRAM devices. We design three programming schemes: a baseline multi-pulse scheme, a single short-pulse scheme, and a single long-pulse scheme. By comparing the programming statistics of the one-transistor-one-resistor (1T1R) structures under different schemes and analyzing their evolution over time, we propose the hypothesis that the number and width of pulses influence the filament size and internal distribution of oxygen vacancies, and thus the short-term stability of ReRAM devices. We employ three-dimensional Kinetic Monte Carlo simulation, constructing filaments of varying sizes and adjusting the oxygen vacancy distribution to simulate the outcomes of different programming schemes. The simulation results align with experimental findings. Based on existing experimental data and modeling studies, we propose programming strategies that balance programmability and reliability for VCM-based filamentary ReRAM devices.