We have investigated a magneto-optical (MO) isolator fabricated by µ-transfer printing (µ-TP) method which enables tiny bonding area with a low-temperature process. Although excessive absorption loss can be reduced, the large junction loss at the boundaries of MO material cladding is still a problem. We propose two ultra-low-loss Mach-Zehnder interferometer-type MO isolators. The tapered coupon type isolator reduces the junction loss of TM mode. The TE input type isolator reduces the junction loss by propagation of TE mode instead of TM mode. We designed these structures and numerically demonstrated ultra-low-loss isolators with insertion losses of <2dB.