Torque teno sus virus (TTSuV) has been detected in pigs with and without diseases. As China’s pig population is booming, it’s important to understand the prevalence of TTSuV in healthy pigs. The aim of this study was to systematically investigate the TTSuV prevalence rate in healthy pigs of different age groups, reared in intensive farms in the Hunan province of China. We detected TTSuV in 401 sera samples of healthy pigs by using PCR with primers located in the untranslated region (UTR). The positive prevalence rates of TTSuVs, TTSuV1, TTSuV2, and co-infection with TTSuV1 and TTSuV2 were calculated. The nucleotide identities of TTSuV1 and TTSuV2 between the reference and obtained sequences were calculated using the P-distance method, and maximum likelihood phylogenetic trees were created using MEGA6.0. TTSuVs were detected with an average frequency of 32.17%, while the frequencies of TTSuV1, TTSuV2, and co-infection with both TTSuV genogroups were 7.99%, 28.92%, and 4.74%, respectively. TTSuV1 and TTSuV2 were detected in pigs mainly in the age range of 12–16 weeks (positive rate >10%) and 8–18 weeks (positive rate >40%), respectively. The nucleotide identities ranged from 92.9%~97.3% for TTSuV1 and 64.7%~99% for TTSuV2 among the obtained sequences. We also observed diversity in TTSuVs based on the phylogenetic analysis of the UTR of the gene. Thus, our study shows the importance of understanding the distribution of TTSuV, which are potentially pathogenic agents in healthy pigs.