In assisted reproductive technology, in vitro fertilization involves cultivating embryos in an artificial environment, often yielding lower-quality embryos compared to in vivo conditions. This study investigated core body temperature (CBT) fluctuations in mice during early pregnancy. Their CBT was measured with a high temporal resolution to identify the optimal thermal conditions during the first five days post-fertilization, aiming to improve in vitro culture conditions. Data were collected from 12 female mice, with 8 becoming pregnant, using temperature loggers every minute for 11 days. Data analysis focused on trends, circadian rhythms, frequency components, and complexity using multiscale entropy (MSE). The results for the pregnant mice showed a mean CBT increase from 37.23 °C to 37.56 °C post-mating, primarily during the light phase, with a significant average rise of 0.58 °C. A Fourier analysis identified dominant 24, 12, 8, and 6 h components, with the 24 h component decreasing by 57%. Irregular fluctuations decreased, and MSE indicated increased complexity in the CBT time series post-mating. These results suggest that reducing diurnal temperature variations and maintaining a slightly elevated mean CBT of approximately 37.5 °C, with controlled minor fluctuations, may enhance embryo quality in pregnant mice. This study provides a reference for temperature regulation in embryo culture, improving embryo quality by aligning in vitro conditions with the natural thermal environment of the fallopian tubes.