Continuous phase modulation (CPM) has the characteristics of high power efficiency, spectral efficiency, and less out-of-band radiation, which is very suitable for the Compass S-band (2483.5–2500 MHz) with limited power and bandwidth. However, as more and more navigation systems share the S-band, the mutual interference between different systems is gradually increasing, and the compatibility of CPM signals with rectangular or raised cosine pulses needs to be further improved. To enhance the navigation performance and compatibility of current CPM candidate signals, we propose to apply continuous phase modulation with prolate spheroidal wave function (CPM-PSWF) to S-band navigation. The proposed modulation scheme selects PSWF with excellent time-frequency energy aggregation and flexible time-bandwidth product as the frequency pulse function of CPM. Then, the influence of key modulation parameters such as M, L, h, and C on CPM-PSWF power spectral density is analyzed, and a specific partial-response CPM-PSWF signal is proposed as the S-band candidate navigation signal. Finally, the navigation performance evaluation criteria are derived, and the proposed signal scheme and existing candidate schemes are comprehensively evaluated. Theoretical analysis and simulation results indicate that compared with CPM with BM2RC(8), cos-phase binary offset carrier (BOCc(4,4)), sin-phase binary offset carrier (BOCs(4,4)), minimum shift keying-BOCs (MSK-BOCs(4,4)) and binary offset carrier (BPSK(8)), the proposed signal scheme not only delivers exceptional spectral performance but also exhibits superior performance in code tracking accuracy and multipath suppression. In addition, in the acquisition and tracking phase, compared with other candidate signals except for BOCc(4,4), the mutual interference between the proposed signal scheme and most S-band signals is the lowest, which is easier to realize the compatibility of the Compass system with IRNSS, Galileo, and Globalstar systems.