In high mobility environment, the carrier frequency offset (CFO) introduced by Doppler shifts can severely degrade the system performance. On the other hand, orthogonal pilot sequence which is utilized in conventional frame structure for CFO and channel estimation induces large pilot resource consumption as the number of users increases, resulting in low achievable throughput. In this paper, we propose CFO and the uplink channel estimation scheme with semi-orthogonal pilot sequence to improve achievable throughput in multi-user massive multiple-input multiple-output (MIMO) systems. Frame structure with semi-orthogonal pilot sequence is implemented with simultaneous data and pilot sequence. In our proposed scheme, we employ successive interference cancellation (SIC) to distinguish between data and pilot sequence. We demonstrate from simulation results that our proposed estimation scheme can enhance the achievable throughput compared to the conventional one in high mobility situations.