Trace element additives are widely supplemented in animal feed to improve growth and reproductive performance, especially for pregnant sows. Although organic trace elements significantly improved production performance compared with inorganic form due to the better bioavailability, antioxidant and immune-promoting function, reports on comparison of the effects on different ligands is still limited. And it is not known that microelement methionine hydroxy analogue chelate (MHAC) whether has similar or even better bioavailability than amino acid chelate (AAC). Thus, the Zn, Cu and Mn chelated with methionine hydroxy analogue (Zn-, Cu- and Mn-MHAC) and amino acid chelate (AAC) were compared in two large-scaled farms under similar conditions. The results showed Zn-, Cu- and Mn-MHAC trace elements significantly increased reproductive performance of Landrace × Yorkshire (LY) 1st sows in treatment farm related to litter size and weight while reduced all adverse pregnancy outcomes (P < 0.001) not only in partial application period but also in full application period compared with historical period, especially in live litter size (P < 0.001), healthy litter size (P < 0.001) and litter weight (P < 0.001), and the increase of birth average weight more than 100g. Treatment farm has similar-level (P > 0.05) even significantly better production performance included litter size (P = 0.003), live litter size (P = 0.039) and mummies (P = 0.011) compared to the control farm in the end of trial period which was much worse than that of control farm in historical period (P < 0.001). In addition, all production performance of treatment farm had a continuous upward trend while control farm showed instability and decreasing trend. Our research revealed Zn-, Cu- and Mn-MHAC may have better effect on improving the performance of sows compared to amino acid chelate (AAC).