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The intricately fluctuating onset of respiratory and circulatory diseases displays rhythms of multi-scaled meteorological conditions due to their sensitivity to weather changes. The intrinsic meteorological rhythms of these diseases are revealed in this bio-meteorological study via Fourier decomposition and harmonic analysis. Daily emergency room (ER) visit data for respiratory and circulatory diseases from three comprehensive hospitals in Haidian district of Beijing, China were used in the analysis. Meteorological data included three temperature metrics, relative humidity, sunshine duration, daily mean air pressure, and wind speed. The Fourier decomposition and harmonic analysis on ER visits and meteorological variables involve frequency, period, and power of all harmonics. The results indicated that: i) for respiratory morbidity, a strong climatic annual rhythm responding to annual temperature change was firstly revealed; its ratio of spectral density was 16–33%. Moreover, significant correlations existed between the high-frequency fluctuations (, Harmonic spectrum; Fourier decomposition; Chronic disease; Climatic cycle; Short-term weather; Meteorology; Climatology; Environmental health; Epidemiology; Circulatory system; Respiratory system, Environmental science.