Concomitant with the opioid epidemic, there has been a rise in pregnant women diagnosed with opioid use disorder and cases of infants born with neonatal opioid withdrawal syndrome (NOWS). NOWS refers to signs and symptoms following cessation of prenatal opioid exposure that comprise neurological, gastrointestinal, and autonomic system dysfunction. A critical indicator of NOWS severity is excessive, high-pitched crying. However, NOWS evaluation is, in large part, subjective, and additional cry features may not be easily recognized during clinical assessment. Thus, there is a need for more objective measures to determine NOWS severity. We used a third trimester-approximate opioid exposure paradigm to model NOWS traits in genetically similar inbred substrains of FVB/N mice (NJ, NCrl, NHsd, and NTac). Pups were injected twice daily from postnatal day 1 (P1) to P14 with morphine (10 mg/kg, s.c.) or saline (20 ml/g, s.c.). Because there were only very minor substrain differences in spontaneous withdrawal-induced ultrasonic vocalization (USV) profiles, we collapsed across substrains to evaluate the effects of morphine withdrawal on additional USV properties. We identified syllable sequences unique to morphine-withdrawn and saline-control FVB/N pups on P7 and P14. We also observed an effect of spontaneous morphine withdrawal on the acoustic properties of USVs and specific syllables on P7 and P14. Multiple withdrawal traits correlated with some acoustic properties of USVs and syllable type emission in morphine-withdrawn FVB/N pups on P7 and P14. These data provide an in-depth investigation of mouse USV syllable profiles and acoustic features during spontaneous neonatal opioid withdrawal in mice.