Objective The aim of this study was to observe the dynamic changes of serum and bone marrow levels of alkaline phosphatase (ALP) in ovariectomized (OVX) rats. Methods Eighty 3-month-old non-pregnant female Sprague Dawley rats were randomly divided into following groups by body weight: baseline group, sham-operation (Sham), and ovariectomized (OVX) rat groups. The rats were killed at 0, 3, 6, 12 or 24 weeks after operation. The changes of serum and bone marrow alkaline phosphatase (ALP) levels were detected with photometer-721 and the number of ALP-positive bone marrow cells was detected with a research grade upright fluorescence microscope. Results In the sham group, the serum ALP levels were significantly increased in the weeks 3 until the week 6. However, the serum ALP levels were significantly decreased in the week 12 until the week 24. The ALP-positive cell number in the bone marrow was significantly increased in the week 3 until week 12, but significantly decreased in the week 24. In the OVX group, the serum ALP levels were significantly increased in the week 3, but significantly decreased in the week 6 until the week 24. The number of ALP-positive bone marrow cells was significantly decreased in the week 3 until the week 24. In addition, the serum ALP levels in the OVX group were significantly higher than that of the sham group. However, the number of ALP-positive bone marrow cells was significantly lower than that of the sham group. Conclusions The change tendency of serum ALP in the sham group is similar with that of bone marrow cells. But the change tendency of serum ALP in OVX rats is different from that of bone marrow cells.