Variable stroke (or compression ratio) has been expected as a potential technology for optimizing engine combustion all the time. The free piston motion of linear engines introduced by its unconstrained dynamics is well suited for this expectation. This paper introduces a numerical analysis to explore the effects of variable stroke operation on the combustion and heat release of a linear hydrogen engine (LHE). A system model which couples zero-dimensional dynamics, multi-dimensional combustion, and one-dimensional gas exchange is established and verified experimentally to predict the combustion of the LHE, and then a series of simulations are performed over a range of motion stroke from 62 mm to 72 mm in 2 mm interval to evaluate its effect on LHE combustion. Results indicates that short stroke operation of the LHE shows obvious advantages in thermal efficiency and high peak combustion pressure, although the completion level of hydrogen combustion is slightly poor. Fast combustion, large heat release, and low level of post combustion effect can be obtained by neither lengthening nor shortening from the certain stroke length of 68 mm, while serious NO emission is indicated. Long-stroke operation makes the LHE clean, although it induces slow engine speed, low thermal efficiency and output power. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.