Damaged rock mass contains a great number of microstructures and defects at various scales, which could influence wave propagation significantly. In this paper, investigation of low-amplitude stress wave attenuation in rocks with different damage degrees was undertaken to determine the effects of parameters including damage degree, heterogeneity and type of waveforms on wave propagation, attenuation and slowness. The numerical method was validated through comparison with laboratory measurements. The damage was induced by conducting uniaxial compression tests on the intact rocks and was defined with the acoustic emission. The results showed that the attenuation ratio of low-amplitude stress wave increases with increasing rock damage degree. The rock heterogeneity was incorporated into the numerical model using a digital image processing technique with the combination of X-ray micro-computerized tomography. We found that the rock heterogeneity has great influence on the wave amplitude attenuation. Three types of waveforms, i.e., half-sine wave, square wave and exponential decay wave, were utilized to analyze influences of waveforms on attenuation characteristics in damaged rock specimens. The attenuation ratio of the exponential decay wave is the highest for rock specimens with the same damage degree, attributed to its highest dominant frequency. Moreover, detailed spectrum analysis suggested that the dominant frequency of the wave signal decreases with increasing damage degree. Based on derived simulating results, an improved classification scheme for determining rock fracturing degree, which groups the rock into zones of slightly fractures, moderately fractured and strongly fractured, was established by considering the relationship between wave amplitude and damage, since wave amplitude, other than wave velocity, is more sensitive to rock damage. The findings in this paper could facilitate a better understanding of wave propagation through rock and provide another means to determine rock fracturing degree.