Companion animals including dogs are one of the important components in One Health. Parasites may cause not only diseases in pet animals but also many zoonotic diseases infecting humans. In this study, we performed a survey of intestinal parasites in fecal specimens (n = 485) collected from outpatient pet dogs with diarrhea in Beijing, China, for the entire year of 2015 by microscopic examination (all parasites) and SSU rRNA-based nested PCR detection (Giardia and Cryptosporidium). We observed a total of 124 (25.6%) parasite-positive specimens that contained one or more parasites, including Giardia duodenalis (12.8%), Cryptosporidium spp. (4.9%), Cystoisospora spp. (4.3%), trichomonads (4.3%), Toxocara canis (3.5%), Trichuris vulpis (0.6%), and Dipylidium caninum (0.2%). Among the 55 dog breeds, infection rates were significantly higher in border collies and bulldogs, but lower in poodles (p < 0.05). Risk factor analysis suggested that age was negatively correlated with the infection rate (p < 0.00001), while vaccination and deworming in the past 12 months could significantly reduce the parasite infections (p < 0.01). Among the 62 Giardia-positive specimens, 21 were successfully assigned into assemblages using glutamate dehydrogenase (gdh) and/or beta-giardin (bg) genes, including assemblage D (n = 15), C (n = 5), and F (n = 1). Among the 24 Cryptosporidium-positive specimens by SSU rRNA PCR, 20 PCR amplicons could be sequenced and identified as Cryptosporidium canis (n = 20). Collectively, this study indicates that parasites are a significant group of pathogens in companion dogs in Beijing, and companion dogs may potentially transmit certain zoonotic parasites to humans, particularly those with weak or weakened immunity.