We studied livestock abortion and various associated risk factors in the Ili region of northwest China. Livestock abortion prevalence was estimated and correlated with infections (Brucellosis, Salmonellosis,
Mycoplasma
and
Chlamydia
seropositivity) and management (farming type and contact with other herds/flocks) risk factors. A total of 2996 serum samples (1406 cow, 1590 sheep) were identified by RBPT (Rose Bengal Plate Test) and c-ELISA (competitive-enzyme linked immunosorbent assay), and they showed the overall seroprevalence of brucellosis in the study area was cow 6.76%, sheep 9.50%. The seroprevalence of brucellosis in X county was cow 7.06%, sheep 9.12%; in H county was cow 11.70%, sheep 10.80%; and in Q county was cow 4.22%, sheep 9.11%. The overall seroprevalence of
Mycoplasma
in the study area was cow 3.20%, sheep 6.42%. The seroprevalence of
Mycoplasma
in X county was cow 3.39%, sheep 7.98%; in H county was cow 5.26%, sheep 9.97%; and in Q county was cow 2.11%, sheep 4.33%. The Odds ratio of brucellosis for cow and sheep, respectively, were 45.909 [95% CI 26.912–78.317,
P
<0.001] and 70.507 [95% CI 43.783–113.544,
P
<0.001] times higher than other abortion-related factors including mixed farming, contact with other flocks and
Mycoplasma
infection. A total of 54 samples, including aborted cow (22), sheep (30) fetuses and milk samples (2), were identified as
Brucella melitensis
(
B
.
melitensis
) positive. A total of 38
Brucella
were isolated from 16 aborted cow, 20 sheep fetuses and 2 milk samples. All of these isolates were identified, and confirmed, as
B
.
melitensis
. A phylogenetic tree showed that the
Brucella
isolates closely matched the
B
.
melitensis
biovar 3 isolated in Inner Mongolia, China, and
B
.
melitensis
isolated from Norway and India. These results suggest that
B
.
melitensis
biovar 3 is the main pathogen responsible for cow and sheep abortion and also pose a human health risk. Additionally, livestock reproduction can also be influenced by
Mycoplasma
infection and managerial factors (farming type and contact with other herds/flocks), especially in remote areas.