Cryptosporidium spp. are important zoonotic parasite causing gastrointestinal diseases in humans and animals. Cattle are major hosts for Cryptosporidium species such as C. parvum, C. bovis, C. ryanae, and C. andersoni, with C. parvum being the most pathogenic and a key zoonotic agent. However, systematic epidemiological data on Cryptosporidium in dairy cattle from Anhui Province remain scarce. This study aims to investigate its prevalence and genetic diversity to support effective control strategies. Cryptosporidium species and subtypes were identified using the small subunit ribosomal RNA (SSU rRNA) and 60 kDa glycoprotein (gp60) genes. PCR testing revealed an overall Cryptosporidium infection rate of 35.4% (338/956) across four dairy farms in Anhui Province, with significant regional variation (p < 0.01). Bengbu exhibited the highest infection rate (61.5%), while Fuyang showed the lowest (8.6%). Age-specific distribution indicated that calves aged 2-6 months had the highest infection rate (50.2%). Four Cryptosporidium spp. were identified: C. parvum, C. andersoni, C. ryanae, and C. bovis, with C. parvum and C. bovis being predominant. The IId subtype family dominated C. parvum isolates. Seven gp60 subtypes were detected in C. ryanae, and five distinct subtypes were identified in C. bovis. The study revealed distinct geographical and age-associated variations in bovine cryptosporidiosis in Anhui Province, highlighting the need for targeted control strategies in high-risk regions and young calves.