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Simple Summary: Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are among the most common diarrhea-causing pathogens in humans and livestock. This was the first study to systematically and molecularly detect the prevalence of three intestinal protozoa in cattle in Heilongjiang Province, Northeast China. Our findings indicate that a variety of species/genotypes are prevalent in cattle in Heilongjiang Province and that some of them are zoonotic, indicating a risk of zoonotic disease transmission in endemic areas. This study helps to understand the epidemiology of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in cattle in Heilongjiang Province. Crytosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are important diarrheal pathogens with a global distribution that threatens the health of humans and animals. Despite cattle being potential transmission hosts of these protozoans, the associated risks to public health have been neglected. In the present study, a total of 1155 cattle fecal samples were collected from 13 administrative regions of Heilongjiang Province. The prevalence of Cryptosporidium spp., G. duodenalis, and E. bieneusi were 5.5% (64/1155; 95% CI: 4.2–6.9), 3.8% (44/1155; 95% CI: 2.7–4.9), and 6.5% (75/1155; 95% CI: 5.1–7.9), respectively. Among these positive fecal samples, five Cryptosporidium species (C. andersoni, C. bovis, C. ryanae, C. parvum, and C. occultus), two G. duodenalis assemblages (E and A), and eight E. bieneusi genotypes (BEB4, BEB6, BEB8, J, I, CHS7, CHS8, and COS-I) were identified. Phylogenetic analysis showed that all eight genotypes of E. bieneusi identified in the present study belonged to group 2. It is worth noting that some species/genotypes of these intestinal protozoans are zoonotic, suggesting a risk of zoonotic disease transmission in endemic areas. The findings expanded our understanding of the genetic composition and zoonotic potential of Cryptosporidium spp., G. duodenalis, and E. bieneusi in cattle in Heilongjiang Province. [ABSTRACT FROM AUTHOR]