Background All plan verification systems available for particle therapy are designed for pre-treatment verification. The plan delivery accuracy during treatment are unknown. The purpose of this study is to introduce a verification method and develop a software for proton and carbon ion plan delivery accuracy check. Methods A program was developed using Matlab to reconstruct dose from beam parameters recorded in log files and compare the dose reconstructed with the dose calculated by treatment planning system (TPS). Ten carbon ion plans and ten proton plans were enrolled in this study for algorithm validation, sensitivity analysis and plan delivery verification. The dose reconstruction algorithm was validated by comparing the dose calculated by TPS with reconstructed dose using the same beam parameters. The sensitivity of gamma pass rate to spot size deviation, position deviation and particle number deviation were analyzed by comparing dose reconstructed from pseudo plans which have manually added errors with original plan dose. Then plan delivery verification using homemade software were done for the 20 actual treated plans. Results A program for plan delivery verification was developed. For the validation of dose reconstruction algorithm, the mean dose difference between reconstructed dose and plan dose were 0.70% ± 0.24% and 0.51% ± 0.25% for carbon ion and proton plans, respectively. According to our simulation, the Gamma pass rate of carbon ion beam is more sensitive to spot position deviation and particle number deviation, and the Gamma pass rate of proton beam is more sensitive to spot size deviation. For the actual plan delivery verification using homemade software, the mean gamma pass rate were 99.47% ± 0.48%, 99.36% ± 0.50% and 99.48% ± 0.50% for carbon ion beams and 99.92% ± 0.13%, 99.96% ±0.06% and 99.89% ±0.13% for proton beams at three different depth of high dose region using 3mm/3% criteria. Conclusions A software was programed and the algorithm was verified. The method we introduced and the software we made for plan delivery verification is feasible and reliable. The verification method presented in this study can be easily repeated in other hospital.