Public pastures in Japan are intended for cattle grazing. However, they suffer significant damage due to Sika deer intrusion. Our goal is to control the behavior of cattle and Sika deer that coexist on public pastures by using their respective languages. This technology is available to public pasture managers. For example, it can simplify the task of gathering cattle, which traditionally requires significant time and effort, while also potentially preventing deer from entering from outside. However, the acoustic characteristics of their vocalizations remain poorly understood. This study investigated the effects of acoustic factors on intraspecific variation in the emergency calls of calves and alarm calls of Sika deer. Each vocalization was analyzed using Praat Phonetic Analysis software, and acoustic parameters were quantified using waveform shape and spectrogram analysis. Twenty-nine parameters, including call duration and fundamental frequencies, were compared across intraspecific variations. Individual differences in the emergency calls of calves were examined, while cluster differences in the alarm calls of Sika deer were examined following cluster classification. There were significant differences in the acoustic parameters of emergency and alarm calls. Each voice was discriminated with a 100% correct response rate. The intraspecific variation was 86.7% for calves’ emergency calls and 96.0% for Sika deer alarm calls. Multiple regression analysis identified that parameters such as formants 2, 4, and 5, and the degree of voice breaks, affected intraspecific differences in the emergency calls of calves, whereas parameters such as formants 1 and 2, and bandwidths 2 and 3, affected the alarm calls of Sika deer. The respective coefficients of determination, R² (adjusted), were 0.58 (P < 0.001) for calves and 0.79 (P < 0.001) for Sika deer. This study suggests that although the acoustic factors affecting intraspecific variation differ between calls with different meanings, formant 2 is common to both.