Inflammation, nutrition, and coagulation play significant roles in cancer prognosis. Autonomic function is also actively involved in tumorigenesis. Previous studies have shown that an elevated C-reactive protein (CRP) level, a serum marker for inflammation, is associated with low heart rate variability (HRV), a common clinical tool for the assessment of autonomic function. It is yet to be investigated whether HRV links to these prognostic factors in cancer patients. Sixty-one patients who were first diagnosed with gastric cancer (GC) were enrolled in this study. Fasting blood samples were collected in the morning seven days before surgery. Blood CRP, prealbumin (PA), and fibrinogen (FIB) were used to assess the inflammation level, nutritional status, and coagulation function respectively. Five-minute resting electrocardiogram (ECG) signals were collected one day before surgical treatment. Short-term HRV time-series were extracted from ECG recordings and were analyzed using commonly-used time- and frequency-domain parameters including standard deviation of normal-to-normal intervals (SDNN), root mean square of successive heartbeat interval differences (RMSSD), very-low-frequency power (VLF), low-frequency power (LF), high-frequency power (HF), total power (TP), LF power in normalized units (LF n.u.), HF power in normalized units (HF n.u.), and ratio of LF to HF (LF/HF). After adjusted for sex, age, body mass index, alcohol consumption, history of diabetes, left ventricular ejection fraction, and hemoglobin levels, our results demonstrated negative associations of HRV with levels of CRP and FIB, while positive associations between HRV and PA level, with effect sizes of as high as 35%–52% standard deviations (SD) changes in CRP, FIB, or PA per 1-SD change in HRV parameters. Therefore, decreased HRV in patients with GC predicts increased burdens of inflammation and coagulation and perturbed nutrition, suggesting that short-term HRV measurement can potentially be a noninvasive biomarker for GC prognosis.