Objective. To investigate the feasibility and correlation of sacroiliac joint (SIJ) fat fraction (FF) and R2
∗
as markers of bone metabolism in patients with ankylosing spondylitis (AS). Methods. 75 AS patients were classified into an early active group (EA), late active group (LA), and inactive group (IA). Additionally, 54 matched healthy individuals were selected to be part of the normal control group (NC). All participants underwent chemical shift encoded based MRI (IDEAL-IQ) and routine clinical SIJ MRI at 3.0 T. FF and R2
∗
were measured in subchondral bone, bone marrow edema (BME), and fat metaplasia (FM). Out of the participants, 39 with BME lesions (15 from EA, 16 from LA, 8 from IA) and 39 with FM lesions (9 from EA, 17 from LA, 13 from IA) were included. Differences in FF, R2
∗
value for subchondral bone of all participants and for BME, FM lesions were evaluated. Subsequently, different stages of BME and FM in patient groups were compared, and the relationship between FF and R2
∗
was analyzed. Results. A significant difference in FF was demonstrated among the BME, FM and the normal bone marrow (
p
<
0.001
), meanwhile, the difference of R2
∗
value in FM was significantly lower (
p
=
0.034
, 0.012) than that of BME and that of normal bone marrow. At lever of different lesions, only the FF for BME was significantly different among 3 patient groups (
p
=
0.001
), while there was no significantly different FF for FM among 3 patient groups. Unlike in BME lesions, the FF in FM lesions had a negative correlation with R2
∗
(
p
<
0.001
,
r
=
−
0.488
). Conclusion. FF and R2
∗
measurements help to quantitatively analyze the bone marrow fat composition and bony trabecular microstructure changes in AS, providing a noninvasive and accurate assessment basis for AS bone metabolism abnormalities.