Modifications to quark and antiquark fragmentation functions due to quark-quark (antiquark) double scattering in nuclear medium are studied systematically up to order O(α 2 s ) in deeply inelastic scattering (DIS) off nuclear targets. At the order O(α 2 s ), twist-four contributions from quark-quark (antiquark) rescattering also exhibit the Landau-Pomeranchuk-Migdal (LPM) interference feature similar to gluon bremsstrahlung induced by multiple parton scattering. Compared to quark-gluon scattering, the modification, which is dominated by t-channel quark-quark (antiquark) scattering, is only smaller by a factor of C F /C A = 4/9 times the ratio of quark and gluon distributions in the medium. Such a modification is not negligible for realistic kinematics and finite medium size. The modifications to quark (antiquark) fragmentation functions from quark-antiquark annihilation processes are shown to be determined by the antiquark (quark) distribution density in the medium. The asymmetry in quark and antiquark distributions in nuclei will lead to different modifications of quark and antiquark fragmentation functions inside a nucleus, which qualitatively explains the experimentally observed flavor dependence of the leading hadron suppression in semi-inclusive DIS off nuclear targets. The quark-antiquark annihilation processes also mix quark and gluon fragmentation functions in the large fractional momentum region, leading to a flavor dependence of jet quenching in heavy-ion collisions.